10-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-K

x ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2012

OR

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from             to            

Commission File Number 000-14656

REPLIGEN CORPORATION

(Exact name of registrant as specified in its charter)

Delaware	04-2729386
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
41 Seyon Street, Bldg. 1, Suite 100 Waltham, MA	02453
(Address of principal executive offices)	(Zip Code)

Registrant’s telephone number, including area code: (781) 250-0111

Securities registered pursuant to Section 12(b) of the Act:

Title of Each Class

Common Stock, $0.01 Par Value Per Share

Name of Exchange on Which Registered

The NASDAQ Stock Market LLC

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes  ¨    No  x.

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ¨    No  x.

Indicate by checkmark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨.

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Website, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    No  ¨.

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K (§229.405 of this chapter) is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  x

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer  ¨	Accelerated filer  x	Non-accelerated filer  ¨	Smaller reporting company  ¨
		(Do not check if a smaller reporting company)

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act).    Yes  ¨    No  x.

The aggregate market value of the voting and non-voting common equity held by non-affiliates as of June 30, 2012, the last business day of the registrant’s most recently completed second fiscal quarter, was $126,339,916.

The number of shares of the registrant’s common stock outstanding as of February 20, 2013 was 31,219,541.

Documents Incorporated By Reference

The registrant intends to file a proxy statement pursuant to Regulation 14A within 120 days of the end of the fiscal year ended December 31, 2012. Portions of such proxy statement are incorporated by reference into Part III of this Annual Report on Form 10-K.

Table of Contents

		PAGE
PART I
Item 1.	Business		1
Item 1A.	Risk Factors		10
Item 1B.	Unresolved Staff Comments		21
Item 2.	Properties		21
Item 3.	Legal Proceedings		21
Item 4.	Mine Safety Disclosures		21
PART II
Item 5.	Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities		22
Item 6.	Selected Consolidated Financial Data		24
Item 7.	Management’s Discussion and Analysis of Financial Condition and Results of Operations		25
Item 7A.	Quantitative and Qualitative Disclosures About Market Risk		41
Item 8.	Financial Statements and Supplementary Data		41
Item 9.	Changes in and Disagreements with Accountants on Accounting and Financial Disclosure		41
Item 9A.	Controls and Procedures		41
Item 9B.	Other Information		44
PART III
PART IV
Item 15.	Exhibits and Financial Statement Schedules		46
SIGNATURES			50

PART I

Item 1. BUSINESS

The following discussion of our business contains forward-looking statements that involve risks and uncertainties. When used in this report, the words “intend,” “anticipate,” “believe,” “estimate,” “plan” and “expect” and similar expressions as they relate to us are included to identify forward-looking statements. Our actual results could differ materially from those anticipated in these forward-looking statements and are a result of certain factors, including those set forth under “Risk Factors” and elsewhere in this Annual Report on Form 10-K.

Overview

Repligen Corporation (“Repligen,” the “Company” or “we”) is a life sciences company that develops, manufactures and markets high-value, consumable bioprocessing products for life sciences companies and biopharmaceutical manufacturing companies worldwide. We are a world-leading manufacturer of both native and recombinant forms of Protein A, critical reagents used in biomanufacturing to separate and purify monoclonal antibodies, a type of biologic drug. We also supply several growth factor products used to increase cell culture productivity during the biomanufacturing process. In the burgeoning area of disposable biomanufacturing technologies, we have developed and currently market a series of OPUS^® (Open-Platform, User-Specified) chromatography columns for use in clinical-scale manufacturing. These pre-packed, “plug-and-play” columns are uniquely flexible and customizable to our customers’ media and size requirements. We generally manufacture and sell Protein A and growth factors to life sciences companies under long-term supply agreements and sell our chromatography columns, as well as media and quality test kits, directly to biopharmaceutical companies or contract manufacturing organizations. We refer to these activities as our bioprocessing business.

On December, 20, 2011, we significantly increased the size of our bioprocessing business through a strategic acquisition. We acquired certain assets and assumed certain liabilities of Novozymes Biopharma Sweden, AB (“Novozymes”) in Lund, Sweden, including the manufacture and supply of cell culture ingredients and Protein A affinity ligands for use in industrial cell culture, stem and therapeutic cell culture and biopharmaceutical manufacturing (the “Novozymes Biopharma Business” and the acquisition of the Novozymes Biopharma Business, the “Novozymes Acquisition”) for a total upfront cash payment of 20.65 million Euros (~$26.9 million). As a result of the Novozymes Acquisition, we nearly doubled the size of our bioprocessing business.

Historically, Repligen also conducted activities aimed at developing proprietary therapeutic drug candidates, often with a potential of entering into a collaboration with a larger commercial stage pharmaceutical or biotechnology company in respect of these programs. In addition, we have out-licensed certain intellectual property to Bristol-Myers Squibb Company, or Bristol, from which we receive royalties on Bristol’s net sales in the United States of their product Orencia^®. As part of our strategic decision in 2012 to focus our efforts on our core bioprocessing business, we scaled back our efforts on our clinical development programs and increased our efforts to find collaboration partners to pursue the development and, if successful, commercialization of these drug programs. The current status of our development portfolio is:

• On December 28, 2012, we out-licensed our SMA program, led by RG3039, to Pfizer Inc., or Pfizer. Pursuant to this license agreement, Pfizer will assume the majority of the costs associated with completing the required clinical trials for this program as well as obtaining U.S. Food and Drug Administration (“FDA”) approval of the respective new drug application (“NDA”). Under the license agreement, we are obligated to conduct additional activities in support of this program, which will include completing the second cohort of the current Phase I trial and supporting the transition of the program to Pfizer. We expect to complete these activities in the first half of 2013.

• The most advanced product candidate in our development portfolio is RG1068, a synthetic human hormone being developed as a novel imaging agent for the improved detection of pancreatic duct

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abnormalities in combination with magnetic resonance imaging in patients with pancreatitis and potentially other pancreatic diseases. We submitted an NDA to the FDA and a marketing authorization application (“MAA”) to the European Medicines Agency (“EMA”) in the first quarter of 2012. In the second quarter of 2012, we received a complete response letter from the FDA, indicating the need for additional clinical efficacy and safety trial data. We are currently working with the FDA on the details of an additional Phase III trial. We believe providing certainty as to the requirements of this additional Phase III trial may be an important factor in the decision by third-parties that may wish to pursue a development or commercialization agreement with us for RG1068.

• Our third clinical development program was targeted at Friedrich’s Ataxia and led by RG2833, a class I histone deacetylase (“HDAC”) inhibitor. RG2833 has received Orphan Drug designation from the FDA and European Commission. We initiated a single, ascending dose Phase 1 study of RG2833 in Friedreich’s Ataxia patients in Italy in the fourth quarter of 2012 and expect to complete this trial in the first half of 2013. We believe the results of this trial may be an important consideration for any third-party that may wish to pursue a development or commercialization agreement with us for RG2833. We expect that any additional development activities that we may pursue in the future will be largely supported by sponsors or collaborators.

• On April 7, 2008, we entered into a settlement agreement with Bristol in connection with a patent infringement lawsuit we filed against Bristol. Under the terms of the agreement, Bristol is obligated to pay us royalties on its U.S. net sales of Orencia^® for any clinical indication at a rate of 1.8% for the first $500,000,000 of annual sales, 2.0% for the next $500,000,000 of annual sales and 4% of annual sales in excess of $1 billion. Under the terms of the agreement, we will not receive any future royalties on Bristol’s sales of Orencia^® made after December 31, 2013.

Corporate Background

We were incorporated in May 1981, under the laws of the State of Delaware. Our principal executive offices are located at 41 Seyon Street, Waltham, Massachusetts 02453 and our telephone number is (781) 250-0111. We conduct manufacturing in Waltham and at our facility in Lund, Sweden.

Change in Fiscal Year

In 2011 we changed our fiscal year end from March 31 to December 31. This Annual Report on Form 10-K reports our financial results for the twelve-month period from January 1, 2012 through December 31, 2012. This report also includes our financial results for the nine-month periods ending on December 31, 2011 and December 31, 2010 and the twelve-month period ending March 31, 2011.

Currently Marketed Products

We currently sell various commercial bioprocessing products based on Protein A and growth factors, as well as a line of pre-packed chromatography columns and quality test kits, which are used in the production of monoclonal antibodies and other biopharmaceutical products.

Our Products for Biologics Manufacturing

Repligen is a leading manufacturer of consumable bioprocessing products including multiple products based on Protein A, growth factors used in fermentation, quality test kits and chromatography products such as proprietary media and a line of pre-packed chromatography columns. These products are sold to life sciences companies, contract manufacturing organizations and biopharmaceutical companies for use in the production of monoclonal antibodies and other biologic drugs. Demand for our bioprocessing products has grown in concert with the expanding markets for biologics, particularly monoclonal antibodies, as well as a result of adding new product offerings through our acquisition of the Novozymes Biopharma Business in December 2011.

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In 2011, the global biologics market was valued at approximately $160 billion and is expected to grow at a rate in the high single digits annually. Market research indicates that the monoclonal antibody segment comprised approximately 32% of the overall biologics market in 2011 and is growing more rapidly than the overall market. Six of the ten worldwide best-selling drugs in 2012 are monoclonal antibodies and include products such as Enbrel^® and Remicade^® for rheumatoid arthritis and other inflammatory disorders, and Rituxan^® for non-Hodgkin’s lymphoma. There are more than 35 approved monoclonal antibody products and over 350 product candidates currently in clinical development, most of which are manufactured using Protein A.

Repligen has been a leading supplier of Protein A for more than ten years and manufactures five forms of Protein A for major life sciences companies including GE Healthcare and EMD Millipore under long-term supply agreements which extend to dates between 2016 and 2021. To be useful in manufacturing, Protein A is chemically bound to proprietary beads that are manufactured by life sciences companies, such as those mentioned above. These beads provide the rigid support required to use Protein A in the manufacturing process for monoclonal antibodies. The Protein A attached to the beads is known as Protein A chromatography media, which is packed by end-users into cylindrical columns and used to purify monoclonal antibodies. For example, after fermentation of a monoclonal antibody, the broth containing the monoclonal of interest as well as numerous fermentation by-products and contaminants is pumped through a column filled with Protein A chromatography media which selectively binds to and captures the monoclonal antibody. Protein A has a high affinity for the monoclonal antibody and as a result, the antibody stays bound to the Protein A media and the impurities flow through the column. After the impurities are washed away, a change in conditions releases the purified antibody. As a result, the monoclonal antibody product is highly purified and concentrated from a single purification step. Further purification steps are usually necessary to increase purity to a level greater than 98%. Over the past three years, the majority of our product sales have been sales of Protein A products.

Most biopharmaceuticals are produced through mammalian fermentation. In order to spur increased cell growth, manufacturers add growth factors and nutrients to the fermenter. As part of the Novozymes Acquisition, the Company acquired four fermentation and cell culture growth factor products. Among those products is LONG^®R3 IGF-I, a growth factor that is more biologically potent than insulin, and that has been shown to significantly increase recombinant protein production in fermentation applications. LONG^®R3 IGF-I is currently used in the manufacture of nine commercial biopharmaceutical products and is sold under a distribution agreement with Sigma-Aldrich Corporation (“Sigma”) which extends to 2021. Sigma has distribution rights for industrial cell culture applications while Repligen sells the product for use in stem cell and other cell-based therapies. In addition, we acquired long epidermal growth factor (LONG^®EGF) and transforming growth factor alpha (LONG^®TGF-a) supplements for serum-free or low serum culture in cell-based therapy applications, as well as recombinant transferrin (rTransferrin) which has been developed as an iron supplement for cell culture. There may be additional applications for these growth factors in stem cell and other cell-based therapies.

We also sell a number of products used for purification and quality control applications to contract manufacturers and biopharmaceutical companies including: pre-packed, disposable chromatography columns, proprietary Protein A chromatography media and quality test kits. Our pre-packed chromatography columns are sold in a variety of sizes with the customer’s choice of media. This product line consists of patented technology that we acquired from BioFlash Partners, LLC (“BioFlash”) in January 2010 and products/technology that we developed as a result of our internal research and development efforts. We call this line of chromatography products OPUS (Open Platform User Specified). OPUS columns have the potential to improve manufacturing efficiencies and lower costs by reducing time for column packing, validation, set-up and cleaning. In addition, because OPUS columns are “plug-and-play” we believe they offer customers significantly greater manufacturing flexibility when used with other flexible, disposable technologies. In early 2012, we introduced new, process-scale OPUS chromatography columns with diameters of 20cm and 30cm. These new products are well suited for the production of a broad range of clinical trial material and niche commercial products such as orphan biologics.

Our proprietary Protein A chromatography media is used by contract manufacturers and biopharmaceutical companies in a variety of applications, including in the purification of some currently marketed biotherapeutics.

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Customers use our ELISA test kits to ensure that there are minimal levels of residual Protein A in the final bulk drug product.

Research and Development

We have conducted research activities aimed at developing proprietary therapeutic drug candidates in various stages of clinical development often with a potential of entering into a collaboration with a larger commercial stage pharmaceutical or biotechnology company in respect of these programs. As part of our strategic decision to focus the Company’s efforts on our core bioprocessing business, we scaled back our research efforts on our clinical development programs and increased our efforts to find collaboration partners to finish their development and, if successful, commercialize these therapeutic drug candidates. Consequently, we believe that our research and development expenses will be lower in the future. We expect that any research and development activities that we undertake in the future with respect to our therapeutic drug candidates will be limited to those which could support the transition of development and commercialization activities for these programs to potential collaborators. In addition, we expect these activities will be substantially funded by potential sponsors, collaborators or licensees. We intend to focus the majority of our future research and development efforts on developing new bioprocessing products. Specifically, we plan to focus these efforts on our growth factor and chromatography product offerings because we believe those markets may offer a higher rate of growth than the Protein A market.

Therapeutic Product Candidates for Out-license

We currently have two therapeutic development programs available for outlicensing: RG1068, a diagnostic imaging agent for patients with pancreatic abnormalities; and RG2833, an early stage program for the treatment of Friedreich’s Ataxia, a rare muscular disorder.

We completed a Phase 3 clinical trial evaluating the sensitivity and specificity of RG1068 (also known as SecreFlo) in combination with MRI to improve the detection of structural abnormalities of the pancreas relative to MRI alone. Based on the results of this trial, we submitted an NDA to the FDA for RG1068 in December 2011. In April 2012, we received a complete response letter from the FDA requesting additional clinical efficacy and safety trial data to support potential approval of the NDA. In 2012, we also submitted an MAA for RG1068 for review by the EMA in the same initial indication. In connection with our decision to focus on our core bioprocessing business, we withdrew this MAA in the fourth quarter of 2012. We are currently working with the FDA to identify the additional clinical requirements for this product candidate. Other than identifying the additional clinical requirements, we do not anticipate putting significant, additional development efforts into this product candidate unless such efforts are predominantly funded by a licensee or collaborator. In conjunction with this decision, we continue to seek development and commercialization partners for RG1068.

We also have a product candidate, RG2833, a class I HDAC inhibitor, in Phase 1 clinical development for the treatment of Friedreich’s ataxia. Friedreich’s ataxia is an inherited disease that causes progressive damage to the nervous system resulting in symptoms ranging from impaired walking and speech problems to heart disease. To date, the development of RG2833 has been partially funded by several groups including GoFAR, a patient advocacy based in Italy, the Friedreich’s Ataxia Research Alliance (also known as FARA), the Muscular Dystrophy Association, the European Friedreich’s Ataxia Consortium for Translations Studies (also known as EFACTS) and the National Ataxia Foundation (also known as NAF). We initiated a single, ascending dose Phase 1 study in Friedreich’s ataxia patients in Italy in the first quarter of 2012 and expect to complete this trial in the first half of 2013. As part of the program, we developed methods to measure changes in frataxin levels in patient cells for use in our clinical trial which may enable us to gain an early insight into the potential benefit of treating patients with RG2833. Once the trial is complete, we do not anticipate making significant expenditures into this product candidate unless such expenditures are substantially funded by a collaborator or licensee. In conjunction with this decision, we are continuing to seek development and commercialization partners for RG2833.

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We were also developing RG3039 for treatment of patients with spinal muscular atrophy (“SMA”). This program was out-licensed to Pfizer in December 2012. SMA is an inherited neurodegenerative disease in which a defect in the survival motor neuron gene (“SMN”) results in low levels of the protein SMN which leads to progressive damage to motor neurons, loss of muscle function and, in many patients, early death.

SMA Agreement with Pfizer

On December 28, 2012, we entered into an exclusive worldwide licensing agreement (the “License Agreement”) with Pfizer to advance the SMA program, which is led by RG3039 and also includes backup compounds and enabling technologies. Under the terms of the License Agreement, we received $5 million from Pfizer as an upfront payment on January 22, 2013 and are entitled to receive up to $65 million in potential future milestone payments, a portion of which may be owed to third parties. These potential payments are approximately equally divided between milestones related to clinical development and initial commercial sales in specific geographies. In addition, we are entitled to receive royalties on any future sales of RG3039 or any SMA compounds developed under the License Agreement. The License Agreement also provides for tiered and increasing royalty rates which begin in the high single-digits for RG-3039 or lesser amounts for any backup compounds developed under the License Agreement. Our receipt of these royalties is subject to an obligation under an existing in-license agreement and other customary offsets and deductions. Royalties are payable, on a country-by-country basis, for a duration based upon the later of (a) expiration of the licensed patent(s) or (b) a predetermined time after the first commercial sale of the first such product in such country.

Pursuant to this license agreement, Pfizer will assume virtually all of the costs associated with completing the required clinical trials for this program as well as obtaining FDA approval of the respective NDA. Under the license agreement, we are obligated to conduct additional activities in support of this program, which will include completion of the second cohort of the current Phase I trial and supporting the transition of the program to Pfizer. We will also provide specific technology transfer services to Pfizer who will then assume full responsibility for the SMA program moving forward, including the conduct of any registration trials necessary for any product approvals. We expect to complete our work on this program in the first half of 2013. Pfizer may terminate the license agreement at any time for convenience.

Orencia^® (CTLA4-Ig) Royalties

CTLA4 is a key regulator of the activity of the immune system. CTLA4 “turns off” the immune system after it has successfully cleared a bacterial or viral infection by blocking the activation of T-cells, the immune cells responsible for initiating an immune response. In the 1990’s, our collaborators at the University of Michigan and the U.S. Navy demonstrated in animal models that a fusion protein consisting of fragments of CTLA4 and an antibody (“CTLA4-Ig”) could be used to treat certain autoimmune diseases. This research finding resulted in the granting of U.S. patent No. 6,685,941 (“the ‘941 Patent”) covering the treatment of certain autoimmune disorders including rheumatoid arthritis with CTLA4-Ig. CTLA4-Ig’s mechanism of action is different from the current therapies for autoimmune disease or organ transplant rejection, thus, it may provide a treatment for patients who are refractory to existing therapies.

In December 2005, the FDA approved Bristol’s application to market CTLA4-Ig, under the brand name Orencia^®, for treatment of rheumatoid arthritis. In January 2006, Repligen and the University of Michigan jointly filed a lawsuit against Bristol in the United States District Court for the Eastern District of Texas for infringement of the ‘941 Patent. In April 2008, Repligen and the University of Michigan entered into a settlement agreement with Bristol pursuant to which, Bristol made an initial payment of $5 million to us and agreed to pay us royalties on the U.S. net sales of Orencia^® for any clinical indication at a rate of 1.8% for the first $500 million of annual sales, 2.0% for the next $500 million and 4.0% of annual sales in excess of $1 billion for each year from January 1, 2008 until December 31, 2013.

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The ‘941 Patent is owned by the University of Michigan and exclusively licensed to Repligen. In consideration of this exclusive license, Repligen agreed to pay the University of Michigan 15% of all royalty income received from Bristol, after deducting legal expenses. There are no annual or other fees associated with this agreement. As of December 31, 2012, we have paid approximately $7,503,000 to the University of Michigan under this agreement.

Sales and Marketing

We sell our bioprocessing products through our direct sales force, partners such as GE Healthcare, EMD Millipore, Sigma Aldrich and distributors in certain foreign markets.

Segment and Geographic Areas

We have one reportable segment. Segment and geographical information is contained in Note 2, the notes to our consolidated financial statements.

Significant Customers and Geographic Reporting

Customers for our bioprocessing products include major life science companies, contract manufacturing organizations, biopharmaceutical companies, diagnostics companies and laboratory researchers. For the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 and the fiscal year ended March 31, 2011, total revenues from sales to customers in the United States were approximately 46%, 48%, 48% and 50%, respectively. During the same periods, total revenues generated though sales to customers in Sweden were 42%, 44%, 45% and 42%, respectively. For the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 and the fiscal year ended March 31, 2011, royalty revenue from Bristol represented 24%, 37%, 37% and 38% of total revenues, respectively. Our largest bioprocessing customer accounted for 42%, 44%, 45% and 42% of total revenues in the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 and the fiscal year ended March 31, 2011, respectively.

Employees

As of February 20, 2013, we had 120 employees. Of those employees, 92 were engaged in research, development and manufacturing and 28 were in administrative and marketing functions. Each of our employees has signed a confidentiality agreement. None of our U.S. employees are covered by collective bargaining agreements. We have two collective bargaining agreements that cover our 55 employees in Sweden, comprising approximately 46% of our total workforce. The current collective bargaining agreements expire on March 31, 2013. The Company considers its employee relations to be satisfactory.

Patents, Licenses and Proprietary Rights

Repligen considers patents, trade secrets and know-how to be an important element in the protection of our competitive and proprietary position and actively, and selectively, pursues patent protection in the United States and in major countries abroad. As further described below, Repligen owns or has exclusive rights to a number of U.S. patents and U.S. pending patent applications as well as corresponding foreign patents and patent applications. The expiration of key patents owned or licensed by us or the failure of patents to issue on pending patent applications could create increased competition, with potential adverse effects on our business prospects.

Other forms of market protection, including trade secrets, orphan drug status and know-how, are also considered important elements of our proprietary strategy. With regard to protection of trade secrets and know-how, our policy is to require each of our employees, consultants, business partners and major customers to

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execute confidentiality agreements upon the commencement of an employment, consulting, business relationship, or product related audit with us. These agreements provide that all confidential information developed or made known to the other party during the course of the relationship with us is to be kept confidential and not disclosed to third parties except in specific circumstances. In the case of employees and consultants, the agreements generally provide that all inventions conceived by the individual in the course of rendering services to Repligen shall be our exclusive property.

Protein A

We have developed proprietary technology, trade secrets, and know-how relating to the manufacture of recombinant Protein A at a scale and quality standard which is consistent with the requirements of the biopharmaceutical industry. In addition, in April 2010, we were granted U.S. Patent No. 7,691,608 B2, “Nucleic Acids Encoding Recombinant Protein A,” which claims a recombinant gene that encodes a Protein A molecule with an amino acid sequence identical to that of the natural Protein A molecule, which has long been commercialized for bioprocessing applications. This U.S. patent, with the term extension that was granted, will remain in effect until 2028. Foreign equivalents of this patent are being prosecuted outside of the United States.

OPUS

In January 2012, Repligen filed a provisional patent application with the U.S. Patent and Trademark Office (“USPTO”) which covers certain unique features of our OPUS pre-packed columns. Pending claims that relate to these unique features cover the ease and flexibility of column packing, bed height and cleaning that is improved over existing column designs. In January 2013, we filed an international patent cooperation treaty (“PCT”) application as well as a utility application with the USPTO on the basis of the provisional application.

CTLA4-Ig

The ‘941 patent, covering the use of CTLA4-Ig to treat specific autoimmune disorders including rheumatoid arthritis and multiple sclerosis was issued in February 2004. The patent is assigned to the University of Michigan and the U.S. Navy and is exclusively licensed to Repligen. In April 2008, Repligen granted Bristol an exclusive sublicense to this patent, pursuant to which Bristol pays us royalties on its U.S. net sales of its rheumatoid arthritis drug, Orencia^® through December 31, 2013.

Spinal Muscular Atrophy

In 2009, Repligen entered into an exclusive license agreement with a non-profit organization, FSMA, for worldwide rights to patent applications related to compositions and methods for the treatment of spinal muscular atrophy. FSMA had funded the development of these compounds and identified a novel enzyme target (“DcpS”) that these compounds inhibit. In 2011, we were granted U.S. Patent Nos. 7,888,366 and 7,985,755, both entitled “2,4 Diaminoquinazolines for Spinal Muscular Atrophy,” with allowed composition claims that cover both the genus and the species of the chemical structures of the lead clinical candidates. Pursuant to the License Agreement, we licensed all of our intellectual property related to SMA to Pfizer and Pfizer has assumed responsibility for maintaining existing intellectual property and prosecuting new intellectual property relating to this program.

Histone Deacetylase Inhibitors

Repligen has entered into an exclusive license agreement with The Scripps Research Institute for worldwide rights to a patent application claiming compounds and methods for treating Friedreich’s ataxia with inhibitors of histone deacetylase. We have extended this original work and filed additional patent applications which claim both methods and compositions for treating Friedreich’s ataxia. If we are successful in our efforts to enter into a development or commercialization partnership for RG2833, we intend to transfer the prosecution of these patent applications to such partner.

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Competition

Our bioprocessing products compete on the basis of quality, performance, cost effectiveness, and application suitability with numerous established technologies. Additional products using new technologies that may be competitive with our products may also be introduced. Many of the companies selling or developing competitive products have greater financial and human resources, research and development, manufacturing and marketing experience than we do. These companies range in size from large, multi-national companies to small, private emerging growth companies. They may succeed in developing products that are more effective or less costly than any that we may develop. These competitors may also prove to be more successful in their production, marketing and commercialization activities. We cannot be certain that the research, development and commercialization efforts of our competitors will not render any of our existing or potential products obsolete.

Manufacturing

We manufacture five forms of commercial scale Protein A including “native” Protein A for life sciences companies including GE Healthcare and EMD Millipore under long-term supply agreements which expire between 2016 and 2021. Native Protein A is manufactured in Sweden, while the recombinant forms are manufactured in both Waltham and Sweden. We currently manufacture our growth factor products in Sweden and assemble and pack our pre-packed chromatography media columns in Waltham.

We generally purchase raw materials from more than one commercially established company and believe that the necessary raw materials are currently commercially available in sufficient quantities necessary to meet market demand. We utilize our own facilities in Waltham and Sweden as well as third party contract manufacturing organizations to carry out certain fermentation and recovery operations, while the purification, immobilization, packaging and quality control testing of our bioprocessing products are conducted at our facilities. Our U.S. facility, located in Waltham, Massachusetts is ISO 9001 certified and maintains a formal quality system to maintain process control, traceability, and product conformance. Our Sweden facility, located in Lund, is cGMP certified. We practice continuous improvement initiatives based on routine internal audits as well as external feedback and audits performed by our partners and customers. In addition, we maintain a business continuity management system which focuses on key areas such as contingency planning, security stocks and off-site storage of raw materials and finished goods to ensure continuous supply of our products.

Government Regulation

The development of drug candidates is subject to regulation in the United States by the FDA and abroad by foreign equivalents. Product development and approval within the FDA regulatory framework usually takes a significant number of years and involves the expenditure of substantial capital resources. Timelines for development are uncertain.

Before clinical testing in the United States of any drug candidate may begin, FDA requirements for preclinical efficacy and safety must be completed. Required toxicity testing typically involves characterization of the drug candidate in several animal species. Safety and efficacy data are submitted to the FDA as part of an IND and are reviewed by the FDA prior to the commencement of human clinical trials.

Clinical trials involve the administration of the drug to human volunteers or patients under the supervision of a qualified investigator, usually a physician, with an FDA-approved protocol. Human clinical trials are typically conducted in three sequential phases:

• Phase 1 clinical trials represent the initial administration of the investigational drug to a small group of human subjects to test for safety (pharmacovigilance), dose tolerability, absorption, biodistribution, metabolism, excretion and clinical pharmacology and, if possible, to gain early evidence regarding efficacy and potential biomarkers.

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• Phase 2 clinical trials typically involve a small sample of the actual intended patient population and seek to assess the efficacy of the drug for specific targeted indications, to determine dose tolerance and the optimal dose range, and to gather additional information relating to safety and potential adverse effects.

• Once an investigational drug is found to have some efficacy and an acceptable safety profile in the targeted patient population, Phase 3 clinical trials are initiated to establish further clinical safety and efficacy of the investigational drug in a broader sample of the general patient population at multiple study sites in order to determine the overall risk-benefit ratio of the drug and to provide an adequate basis for product approval. The Phase 3 clinical development program consists of expanded, large-scale studies of patients with the target disease or disorder to obtain definitive statistical evidence of the efficacy and safety of the proposed product.

All data obtained from a comprehensive development program are submitted in an NDA to the FDA and the corresponding agencies in other countries for review and approval. The NDA includes information pertaining to clinical studies and the manufacture of the new drug. Review of an NDA by the FDA can be a time-consuming process, and the FDA may request that we submit additional data or carry out additional studies.

Available Information

We maintain a website with the address www.repligen.com. We are not including the information contained on our website as a part of, or incorporating it by reference into, this Annual Report on Form 10-K. We make available free of charge through our website our annual reports on Form 10-K, quarterly reports on Form 10-Q and current reports on Form 8-K, and amendments to these reports, as soon as reasonably practicable after we electronically file such materials with, or furnish such materials to, the Securities and Exchange Commission. Our Code of Business Conduct and Ethics is also available free of charge through our website.

In addition, the public may read and copy any materials that we file with the Securities and Exchange Commission at the Securities and Exchange Commission’s Public Reference Room at 100 F Street, NE, Washington, D.C. 20549. The public may obtain information on the operation of the Public Reference Room by calling the Securities and Exchange Commission at 1-800-SEC-0330. Also, our filings with the Securities and Exchange Commission may be accessed through the Securities and Exchange Commission’s Electronic Data Gathering, Analysis and Retrieval (EDGAR) system at www.sec.gov.

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Item 1A. RISK FACTORS

Investors should carefully consider the risk factors described below before making an investment decision.

If any of the events described in the following risk factors occur, our business, financial condition or results of operations could be materially harmed. In that case the trading price of our common stock could decline, and investors may lose all or part of their investment. Additional risks and uncertainties that we are unaware of or that we currently deem immaterial may also become important factors that affect Repligen.

This Annual Report on Form 10-K contains forward looking statements that involve risks and uncertainties. Our actual results could differ materially from those anticipated in these forward looking statements as a result of certain factors, including the risks faced by us described below and elsewhere in this Annual Report on Form 10-K.

We may fail to realize additional benefits from the Novozymes Acquisition.

We will be required to expend additional time and resources in order to realize all of the anticipated synergies, business opportunities and growth prospects that we anticipated at the time of the acquisition of the Novozymes Biopharma Business. We may never fully realize these anticipated synergies, business opportunities and growth prospects. Integrating operations is complex and requires significant efforts and expenditures. Assumptions underlying estimated benefits may be inaccurate and general industry and business conditions might deteriorate. Our management might have its attention diverted while continuing the integration of operations and corporate and administrative infrastructures from the Novozymes architecture into the correlative Repligen systems. If any of these factors limit our ability to fully-integrate our operations with those of the Novozymes Biopharma Business successfully or on a timely basis, the expectations of future results of operations, including synergies and other benefits expected to result from the Novozymes Acquisition, might not be met.

We incurred significant transaction, integration and other costs in connection with the Novozymes Acquisition and these costs may exceed the realized benefits, if any, of the synergies and efficiencies from the acquisition.

We have already incurred significant transaction costs related to the Novozymes Acquisition. In addition, we expect to continue to incur integration costs as we work toward completing the integration of the Novozymes Biopharma Business with our own. Financial, managerial and operational challenges of the Novozymes Acquisition may include:

• challenges associated with managing the larger, more complex, combined business;

• disruption of our ongoing businesses and diversion of management attention;

• difficulties in systems integration, particularly information technology and finance systems, and conforming standards, controls, procedures and policies, business cultures and compensation structures between the entities;

• difficulties in integrating the Novozymes Biopharma Business’ products and technologies;

• disruptions in relationships with customers and suppliers;

• coordinating geographically dispersed organizations;

• risks associated with acquiring intellectual property;

• difficulties in operating the Novozymes Biopharma Business profitably;

• the inability to achieve anticipated synergies, cost savings or growth;

• potential loss of key employees;

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• unanticipated costs; and

• potential disputes with Novozymes Denmark.

No assurances can be given that the expected synergies and other benefits of the Novozymes Acquisition will exceed the transaction and integration costs and the costs associated with these potential financial, managerial and operational challenges, or that expected synergies and other benefits will be achieved in the near term or at all.

If intangible assets that we recorded in connection with the Novozymes Acquisition become impaired, we could have to take significant charges against earnings.

In connection with the accounting for the Novozymes Acquisition, we recorded a significant amount of intangible assets, including developed technology and customer relationships. Under U.S. GAAP, we must assess, at least annually and potentially more frequently, whether the value of intangible assets has been impaired. Intangible assets will be assessed for impairment in the event of an impairment indicator. Any reduction or impairment of the value of intangible assets will result in a charge against earnings, which could materially adversely affect our results of operations and shareholders’ equity in future periods.

Our exposure to political, economic and other risks that arise from operating a multinational business has increased dramatically since the consummation of the Novozymes Acquisition.

Our operations and sales outside of the United States have increased and may continue to increase as a result of the Novozymes Acquisition. Risks related to these increased foreign operations include:

• changes in general economic and political conditions in countries where we operate, particularly as a result of ongoing economic instability within the European Union;

• being subject to complex and restrictive employment and labor laws and regulations, as well as union and works council restrictions;

• fluctuations in foreign currency exchange rates;

• changes in tax laws or rulings in the United States or other foreign jurisdictions that may have an adverse impact on our effective tax rate;

• being subject to burdensome foreign laws and regulations, including regulations that may place an increased tax burden on our operations;

• being subject to longer payment cycles from customers and experiencing greater difficulties in timely accounts receivable collections; and

• required compliance with a variety of foreign laws and regulations.

Our business success depends in part on our ability to anticipate and effectively manage these and other risks to which our exposure has increased following the Novozymes Acquisition. We cannot assure you that these and other related factors will not materially adversely affect our international operations or business as a whole since the consummation of the Novozymes Acquisition.

We may be unable to manage efficiently having become a larger and more geographically diverse organization since the consummation of the Novozymes Acquisition.

Since the acquisition of the Novozymes Biopharma Business, we have faced challenges inherent in efficiently managing an increased number of employees over large geographic distances, including the need to implement appropriate systems, policies, benefits and compliance programs. Our inability to manage successfully the geographically more diverse (including from a cultural perspective) and substantially larger

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combined organization could materially adversely affect our operating results and, as a result, the market price of our common stock.

The environmental risks of our business have increased dramatically since the Novozymes Acquisition.

Our manufacturing business involves the controlled use of hazardous materials and chemicals and is therefore subject to numerous environmental and safety laws and regulations and to periodic inspections for possible violations of these laws and regulations. In addition to these hazardous materials and chemicals, our facility in Sweden, also uses Staphylococcus aureus and toxins produced by Staphylococcus aureus in some of its manufacturing processes. Staphylococcus aureus and the toxins it produces, particularly enterotoxins, can cause severe illness in humans. The costs of compliance with environmental and safety laws and regulations are significant and have increased since we completed the acquisition of the Novozymes Biopharma Business. Any violations, even if inadvertent or accidental, of current or future environmental, safety laws or regulations and the cost of compliance with any resulting order or fine could adversely affect our operations.

Our acquisitions expose us to risks that could adversely affect our business, and we may not achieve the anticipated benefits of acquisitions of businesses or technologies.

In addition to the Novozymes Acquisition and as a part of our growth strategy, we may make selected acquisitions of complementary products and/or businesses. Any acquisition involves numerous risks and operational, financial, and managerial challenges, including the following, any of which could adversely affect our business, financial condition, or results of operations:

• difficulties in integrating new operations, technologies, products, and personnel;

• lack of synergies or the inability to realize expected synergies and cost-savings;

• difficulties in managing geographically dispersed operations;

• underperformance of any acquired technology, product, or business relative to our expectations and the price we paid;

• negative near-term impacts on financial results after an acquisition, including acquisition-related earnings charges;

• the potential loss of key employees, customers, and strategic partners of acquired companies;

• claims by terminated employees and shareholders of acquired companies or other third parties related to the transaction;

• the issuance of dilutive securities, assumption or incurrence of additional debt obligations or expenses, or use of substantial portions of our cash;

• any collaboration, strategic alliance and licensing arrangement may require us to relinquish valuable rights to our technologies or product candidates, or grant licenses on terms that are not favorable to us;

• diversion of management’s attention and company resources from existing operations of the business;

• inconsistencies in standards, controls, procedures, and policies;

• the impairment of intangible assets as a result of technological advancements, or worse-than-expected performance of acquired companies; and

• assumption of, or exposure to, unknown contingent liabilities or liabilities that are difficult to identify or accurately quantify.

In addition, the successful integration of acquired businesses requires significant efforts and expense across all operational areas, including sales and marketing, research and development, manufacturing, finance, legal,

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and information technologies. There can be no assurance that any of the acquisitions we may make will be successful or will be, or will remain, profitable. Our failure to successfully address the foregoing risks may prevent us from achieving the anticipated benefits from any acquisition in a reasonable time frame, or at all.

We face competition from numerous competitors, most of whom have far greater resources than we have, which may make it more difficult for us to achieve significant market penetration.

The bioprocessing market is intensely competitive, subject to rapid change and significantly affected by new product introductions and other market activities of industry participants.

Many of our competitors are large, well-capitalized companies with significantly more market share and resources than we have. As a consequence, they are able to spend more aggressively on product development, marketing, sales and other product initiatives than we can. Many of these competitors have:

• significantly greater name recognition;

• larger and more established distribution networks;

• additional lines of products and the ability to bundle products to offer higher discounts or other incentives to gain a competitive advantage;

• greater experience in conducting research and development, manufacturing, clinical trials, marketing, obtaining regulatory approval and entering into collaboration or other strategic partnership arrangements; and

• greater financial and human resources for product development, sales and marketing and patent litigation.

Our current competitors or other companies may at any time develop additional products that compete with our products. If an existing or future competitor develops products that compete with or are superior to our products, our revenue may decline. In addition, some of our competitors may compete by lowering the price of their products. If prices were to fall, we may not be able to improve our gross margins or sales growth sufficiently to maintain and grow our profitability.

We depend on, and expect to continue to depend on, a limited number of customers for a high percentage of our revenues.

As a result, the loss of, or a significant reduction in orders from, any of these customers would significantly reduce our revenues and harm our results of operations. If a large customer purchases fewer of our products, defers orders or fails to place additional orders with us, our revenue could decline, and our operating results may not meet market expectations. In addition, if those customers order our products, but fail to pay on time or at all, our liquidity and operating results could be materially and adversely affected.

As we evolve from a company involved in research and development to a company with a strategic focus on our bioprocessing business, we may encounter difficulties in expanding our operations successfully.

In connection with the Company’s decision to focus our efforts on the growth of our core bioprocessing business, we will continue to seek development and commercialization partnerships for our remaining portfolio of therapeutic and diagnostic assets. Our future financial performance will depend, in part, on our ability to successfully negotiate and consummate these partnerships. We may not be able to accomplish these tasks, and our failure to accomplish any of them could prevent us from monetizing our clinical stage assets, including RG1068 and RG2833. There is also no guarantee that we will successfully expand our bioprocessing business as a result of this change in strategic focus and the Company’s financial performance will likely suffer if we are unable to do so.

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Our royalty agreement with Bristol-Myers Squibb on sales of Orencia expires on December 31, 2013.

Our royalty agreement with Bristol provides for us to receive payments from Bristol based on their net sales of their Orencia^® product in the United States through December 31, 2013. As a result, we will no longer receive royalty payments under this agreement after December 31, 2013. If we are unable to replace these royalty payments with an alternative source of revenue and related income, our operating results will decline and, as a result, we may experience a decline in the price of our common stock. In addition, we have no control over Bristol’s sales and marketing practices for Orencia^®, and Bristol has no obligation to use commercially reasonable efforts to sell Orencia^®. Bristol’s sales could be significantly impacted by regulatory and market influences beyond our control, resulting in low or even no royalty revenue for us.

We have limited sales and marketing capabilities.

We have a small sales force and, historically, we have generated most of our revenues through sales of bioprocessing products to a limited number of life sciences companies, such as GE Healthcare, EMD Millipore, Sigma-Aldrich, Life Technologies and through other individual distributors. However, we expect a significant amount of our future revenue growth to come from bioprocessing products that we sell directly to end-users such as biopharmaceutical companies and contract manufacturing organizations. This may require us to invest additional resources in our sales and marketing capabilities. We may not be able to attract and retain additional sales and marketing professionals, and the cost of building the sales and marketing function may not generate our anticipated revenue growth. In addition, our sales and marketing efforts may be unsuccessful. Our failure to manage these risks may have a negative impact on our financial condition, or results of operations and may cause our stock price to decline.

If we are unable to obtain, maintain our intellectual property, we may not be able to succeed commercially.

We endeavor to obtain and maintain patent and trade secret protection for our products and processes when available in order to protect them from unauthorized use and to produce a financial return consistent with the significant time and expense required to bring our products to market. Our success will depend, in part, on our ability to:

• obtain and maintain patent protection for our products and manufacturing processes;

• preserve our trade secrets;

• operate without infringing the proprietary rights of third parties; and

• secure any necessary licenses from others on acceptable terms.

We cannot be sure that any patent applications relating to our products that we will file in the future or that any currently pending applications will issue on a timely basis, if ever. Since patent applications in the United States filed prior to November 2000 are maintained in secrecy until patents issue and since publication of discoveries in the scientific or patent literature often lag behind actual discoveries, we cannot be certain that we were the first to make the inventions covered by each of our pending patent applications or that we were the first to file patent applications for such inventions. Even if patents are issued, the degree of protection afforded by such patents will depend upon the:

• scope of the patent claims;

• validity and enforceability of the claims obtained in such patents; and

• our willingness and financial ability to enforce and/or defend them.

The patent position of life sciences companies is often highly uncertain and usually involves complex legal and scientific questions. Patents which may be granted to us in certain foreign countries may be subject to

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opposition proceedings brought by third parties or result in suits by us, which may be costly and result in adverse consequences for us.

In some cases, litigation or other proceedings may be necessary to assert claims of infringement, to enforce patents issued to us or our licensors, to protect trade secrets, know-how or other intellectual property rights we own or to determine the scope and validity of the proprietary rights of third parties. Such litigation could result in substantial cost to us and diversion of our resources. An adverse outcome in any such litigation or proceeding could have a material adverse effect on our business, financial condition and results of operations.

If our competitors prepare and file patent applications in the United States that claim technology also claimed by us, we may be required to participate in interference proceedings declared by the U.S. Patent and Trademark Office to determine priority of invention, which would result in substantial costs to us.

Since some of our U.S. patents covering recombinant Protein A have expired, we may face increased competition, which could harm our results of operations, financial condition, cash flow and future prospects.

Other companies could begin manufacturing and selling recombinant Protein A in the U.S. and may directly compete with us on certain Protein A products. This may induce us to sell Protein A at lower prices and may erode our market share which could adversely affect our results of operations, financial condition, cash flow and future prospects.

Our freedom to develop our products may be challenged by others, and we may have to engage in litigation to determine the scope and validity of competitors’ patents and proprietary rights, which, if we do not prevail, could harm our business, results of operations, financial condition, cash flow and future prospects.

There has been substantial litigation and other proceedings regarding the complex patent and other intellectual property rights in the life sciences industry. We have been a party to, and in the future may become a party to, patent litigation or other proceedings regarding intellectual property rights.

Other types of situations in which we may become involved in patent litigation or other intellectual property proceedings include:

• We may initiate litigation or other proceedings against third parties to seek to invalidate the patents held by such third parties or to obtain a judgment that our products or services do not infringe such third parties’ patents.

• We may initiate litigation or other proceedings against third parties to seek to enforce our patents against infringement.

• If our competitors file patent applications that claim technology also claimed by us, we may participate in interference or opposition proceedings to determine the priority of invention.

• If third parties initiate litigation claiming that our processes or products infringe their patent or other intellectual property rights, we will need to defend against such claims.

The cost to us of any patent litigation or other proceeding, even if resolved in our favor, could be substantial. Some of our competitors may be able to sustain the cost of such litigation or proceedings more effectively than we can because of their substantially greater financial resources. If a patent litigation or other intellectual property proceeding is resolved in a way that is unfavorable to us, we or our collaborative or strategic partners may be enjoined from manufacturing or selling our products and services without a license from the other party and be held liable for significant damages. The failure to obtain any required license on commercially acceptable terms or at all may harm our business, results of operations, financial condition, cash flow and future prospects.

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Uncertainties resulting from the initiation and continuation of patent litigation or other proceedings could have a material adverse effect on our ability to compete in the marketplace. Patent litigation and other proceedings may also absorb significant management time, attention and resources.

We may become involved in litigation or other proceedings with collaborative partners, which may be time consuming, costly and could result in delays in our development and commercialization efforts.

In connection with the Company’s decision to focus its efforts on the growth of its core bioprocessing business, we will seek development and commercialization partnerships for our remaining portfolio of clinical stage assets. Any disputes with such partners that lead to litigation or similar proceedings may result in us incurring legal expenses, as well as facing potential legal liability. Such disputes, litigation or other proceedings are also time consuming and may cause delays in our development and commercialization efforts. If we fail to resolve these disputes quickly and with terms that are no less favorable to us than the current terms of the arrangements, our business, results of operations, financial condition, cash flow and future prospects may be harmed.

If we are unable to continue to hire and retain skilled personnel, then we will have trouble developing and marketing our products.

Our success depends largely upon the continued service of our management and scientific staff and our ability to attract retain and motivate highly skilled technical, scientific, management and marketing personnel. We also face significant competition in the hiring and retention of such personnel from other companies, research and academic institutions, government and other organizations who have superior funding and resources. The loss of key personnel or our inability to hire and retain skilled personnel could materially adversely affect our product development efforts and our business.

The market may not be receptive to our new bioprocessing products upon their introduction.

We expect a portion of our future revenue growth to come from introducing new bioprocessing products, such as a larger size version of our OPUS disposable chromatography products which we began selling in 2012. The commercial success of these new products as well as the products acquired in the Novozymes Acquisition will depend upon their acceptance by the life science and biopharmaceutical industries. Many of the bioprocessing products that we are developing are based upon new technologies or approaches. As a result, there can be no assurance that these new products, even if successfully developed and introduced, will be accepted by customers. If customers do not adopt our new products and technologies, our results of operations may suffer and, as a result, the market price of our common stock may decline.

If our products do not perform as expected or the reliability of the technology on which our products are based is questioned, we could experience lost revenue, delayed or reduced market acceptance of our products, increased costs and damage to our reputation.

Our success depends on the market’s confidence that we can provide reliable, high-quality bioprocessing products. We believe that customers in our target markets are likely to be particularly sensitive to product defects and errors. Our reputation and the public image of our products and technologies may be impaired if our products fail to perform as expected. Although our products are tested prior to shipment, defects or errors could nonetheless occur in our products. Furthermore, the Protein A that we manufacture is subsequently incorporated into products that are sold by other life sciences companies and we have no control over the manufacture and production of those products.

In the future, if our products experience, or are perceived to experience, a material defect or error, this could result in loss or delay of revenues, delayed market acceptance, damaged reputation, diversion of development resources, legal claims, increased insurance costs or increased service and warranty costs, any of which could

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harm our business. Such defects or errors could also narrow the scope of the use of our products, which could hinder our success in the market. Even after any underlying concerns or problems are resolved, any lingering concerns in our target market regarding our technology or any manufacturing defects or performance errors in our products could continue to result in lost revenue, delayed market acceptance, damaged reputation, increased service and warranty costs and claims against us.

If we are unable to manufacture our products in sufficient quantities and in a timely manner, our operating results will be harmed, our ability to generate revenue could be diminished and our gross margin may be negatively impacted.

Our revenues and other operating results will depend in large part on our ability to manufacture and assemble our products in sufficient quantities and in a timely manner. Any interruptions we experience in the manufacturing or shipping of our products could delay our ability to recognize revenues in a particular quarter. Manufacturing problems can and do arise, and as demand for our products increases, any such problems could have an increasingly significant impact on our operating results. While we have not generally experienced problems with or delays in our production capabilities that resulted in delays in our ability to ship finished products, there can be no assurance that we will not encounter such problems in the future. We may not be able to quickly ship products and recognize anticipated revenues for a given period if we experience significant delays in the manufacturing process. In addition, we must maintain sufficient production capacity in order to meet anticipated customer demand, which carries fixed costs that we may not be able to offset if orders slow, which would adversely affect our operating margins. If we are unable to manufacture our products consistently, in sufficient quantities, and on a timely basis, our bioprocessing revenue, gross margins and our other operating results will be materially and adversely affected.

Our operating results may fluctuate significantly, our customers’ future purchases are difficult to predict and any failure to meet financial expectations may result in a decline in our stock price.

Our quarterly operating results may fluctuate in the future as a result of many factors such as the impact of seasonal spending patterns, changes in overall spending levels in the life sciences industry, the inability of some of our customers to consummate anticipated purchases of our products due to changes in end-user demand, and other unpredictable factors that may affect ordering patterns. Because our revenue and operating results are difficult to predict, we believe that period-to-period comparisons of our results of operations are not a good indicator of our future performance. Additionally, if revenue declines in a quarter, whether due to a delay in recognizing expected revenue, adverse economic conditions or otherwise our results of operations will be harmed because many of our expenses are relatively fixed. In particular, a large portion of our manufacturing costs, our research and development, sales and marketing and general and administrative expenses are not significantly affected by variations in revenue. If our quarterly operating results fail to meet investor expectations, the price of our common stock may decline.

We may be unsuccessful in negotiating and consummating development and commercialization partnerships for our remaining portfolio of therapeutic and diagnostic assets on acceptable terms, if at all.

Our decision to focus on the growth of the Company’s core bioprocessing business will result in the Company seeking development or commercialization partners for our remaining portfolio of therapeutic and diagnostic assets. The consummation and performance of any such future development and commercialization transactions will involve risks, such as:

• diversion of managerial resources from day-to-day operations;

• exposure to litigation from the counterparties to any such transaction or other third parties;

• misjudgment with respect to value;

• higher than expected transaction costs; or

• an inability to successfully consummate any such transaction or collaboration.

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Our future revenues pursuant to our license agreement with Pfizer regarding the SMA program depends significantly on Pfizer’s development and commercialization activities, over which we have little control. If Pfizer is unable or determines not to further develop or commercialize the SMA program, or experiences significant delays in doing so, we may see a delay in receiving any potential milestone or royalty payments or fail to receive any additional financial benefits from the program.

We entered into a license agreement with Pfizer on December 28, 2012, related to the SMA program, which is led by RG3039 and also includes backup compounds and enabling technologies. We are dependent on Pfizer for the future success of this development program. Other than assisting in the completion of the first two cohorts of an active Phase 1 trial evaluating RG3039 in healthy volunteers, we will have no future control over the conduct and timing of development efforts with respect to the SMA program. Although we have had discussions with Pfizer regarding their current plans and intentions for the development of the SMA program, they may revise their plan in their sole discretion. Pfizer’s failure to devote sufficient financial and other resources to the development plan may result in the delayed or unsuccessful development of the program, which could lead to the non-payment or delay in payment of milestones under the license agreement and may preclude or delay commercialization of any product under the SMA program and any royalties we could receive on future commercial sales. Because the license we granted to Pfizer is exclusive, our future financial results may be harmed if Pfizer does not commercialize the SMA program successfully or on a timely basis or if Pfizer elects to terminate the license agreement prior to the achievement of any milestones or the payment of any royalties to us.

Healthcare reform measures could adversely affect our business.

The efforts of governmental and third-party payors to contain or reduce the costs of health care may adversely affect the business and financial condition of pharmaceutical and biotechnology companies, including us. Specifically, in both the United States and some foreign jurisdictions, there have been a number of legislative and regulatory proposals to change the health care system in ways that could affect our ability to sell our products profitably. The U.S. Congress passed the America Affordable Health Choices Act of 2009 and is considering a number of proposals that are intended to reduce or limit the growth of health care costs and which could significantly transform the market for pharmaceuticals products. We expect further federal and state proposals and health care reforms to continue to be proposed by legislators, which could limit the prices that can be charged for the products we develop and may limit our commercial opportunity. In the United States, the Medicare Prescription Drug, Improvement, and Modernization Act of 2003, also called the Medicare Modernization Act (the “MMA”) changed the way Medicare covers and pays for pharmaceutical products. These cost reduction initiatives and other provisions of this legislation could decrease the coverage and price that we receive for any approved products and could seriously harm our business. While the MMA applies only to drug benefits for Medicare beneficiaries, private payors often follow Medicare coverage policy and payment limitations in setting their own reimbursement rates, and any reduction in reimbursement that results from the MMA may result in a similar reduction in payments from private payors. The continuing efforts of government and other third-party payors to contain or reduce the costs of health care through various means may limit our commercial opportunities. In addition, the pendency or approval of such proposals could result in a decrease in the price of Repligen’s common stock or limit our ability to raise capital or to enter into collaborations or license rights to our products.

We compete with life science, pharmaceutical and biotechnology companies who are capable of developing new approaches that could make our products and technology obsolete.

The market for therapeutic and commercial products is intensely competitive, rapidly evolving and subject to rapid technological change. Life science, pharmaceutical and biotechnology companies may have substantially greater financial, manufacturing, marketing, and research and development resources than we have. New approaches by these competitors may make our products and technologies obsolete or noncompetitive.

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We may be exposed to liabilities under the Foreign Corrupt Practices Act, and any determination that we violated the Foreign Corrupt Practices Act could have a material adverse effect on our business.

We are subject to the Foreign Corrupt Practice Act (the “FCPA”) and other laws that prohibit improper payments or offers of payments to foreign governments and their officials and political parties by U.S. persons and issuers as defined by the statute for the purpose of obtaining or retaining business. We have operations, agreements with third parties and make sales in jurisdictions outside of the U.S., which may experience corruption. Our activities in jurisdictions outside of the U.S. create the risk of unauthorized payments or offers of payments by one of our employees, consultants, sales agents or distributors, because these parties are not always subject to our control. These risks have increased following the Novozymes Acquisition. It is our policy to implement safeguards to discourage these practices by our employees. However, our existing safeguards and any future improvements may prove to be less than effective, and the employees, consultants, sales agents or distributors of our Company may engage in conduct for which we might be held responsible. Violations of the FCPA may result in severe criminal or civil sanctions, and we may be subject to other liabilities, which could negatively affect our business, operating results and financial condition. In addition, the government may seek to hold us liable for successor liability FCPA violations committed by any companies in which we invest or that we acquire.

Our stock price could be volatile, which could cause shareholders to lose part or all of their investment.

The market price of our common stock, like that of the common stock of many other companies with similar market capitalizations, is highly volatile. In addition, the stock market has experienced extreme price and volume fluctuations. This volatility has significantly affected the market prices of securities of many life sciences, biotechnology and pharmaceutical companies for reasons frequently unrelated to or disproportionate to the operating performance of the specific companies. These broad market fluctuations may adversely affect the market price of our common stock.

Our growth potential is changing as we evolve from an organization that was heavily involved in research and development to an organization with a strategic focus on our bioprocessing business.

In connection with the Company’s decision to focus its efforts on the growth of its core bioprocessing business, the Company expects that its therapeutic product development activities will be significantly reduced. The core bioprocessing business on which the Company will focus will provide growth opportunities that are different than those of a research and development oriented biotechnology company. As a result, the price of the Company’s common stock may behave differently than it has historically and, during the shift in our business, may behave in a manner not expected by securities analysts and investors. If the Company’s future business focused on bioprocessing generates results that fall below the revised expectations of securities analysts and investors, the trading price of the Company’s common stock could decline.

As a result of these risks, we may not be able to achieve the expected benefits of any such transaction or deliver the value thereof to our shareholders. If we are unsuccessful in consummating any such transaction, we may be required to reevaluate our business only after we have incurred substantial expenses and devoted significant management time and resources.

Anti-takeover provisions in our charter documents and under Delaware law could make an acquisition of us, even one that may be beneficial to our stockholders, more difficult and may prevent attempts by our stockholders to replace or remove our current management.

Provisions in our certificate of incorporation and by-laws may delay or prevent an acquisition of us or a change in our management. These provisions include the ability of our board of directors to issue preferred stock without stockholder approval. In addition, because we are incorporated in Delaware, we are governed by the provisions of Section 203 of the Delaware General Corporation Law, which limits the ability of stockholders

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owning in excess of 15% of our outstanding voting stock to merge or combine with us. Although we believe these provisions collectively provide for an opportunity to obtain greater value for stockholders by requiring potential acquirers to negotiate with our board of directors, they would apply even if an offer rejected by our board were considered beneficial by some stockholders. In addition, these provisions may frustrate or prevent any attempts by our stockholders to replace or remove our current management by making it more difficult for stockholders to replace members of our board of directors, which is responsible for appointing the members of our management.

Changes in accounting standards and subjective assumptions, estimates, and judgments by management related to complex accounting matters could significantly affect our financial results or financial condition.

Generally accepted accounting principles and related accounting pronouncements, implementation guidelines, and interpretations with regard to a wide range of matters that are relevant to our business, such as revenue recognition, asset impairment and fair value determinations, inventories, business combinations and intangible asset valuations, and litigation, are highly complex and involve many subjective assumptions, estimates, and judgments. Changes in these rules or their interpretation or changes in underlying assumptions, estimates, or judgments could significantly change our reported or expected financial performance or financial condition.

The Company’s results of operations could be negatively affected by potential fluctuations in foreign currency exchange rates.

The Company conducts a large portion of its business in international markets. For the fiscal year ended December 31, 2012, 28% of the Company’s revenue and 39% of its costs and expenses were denominated in foreign currencies, primarily the Swedish Kroner. Therefore, the Company is exposed to the risk of an increase or decrease in the value of the foreign currencies relative to the U.S. Dollar, which would increase the value of our expenses and decrease the value of our revenue when measured in U.S. Dollars. As a result, our results of operation may be influenced by the effects of future exchange rate fluctuations and such effects may have an adverse impact on our common stock price.

Our ability to use net operating loss and tax credit carryforwards and certain built-in losses to reduce future tax payments is limited by provisions of the Internal Revenue Code, and it is possible that certain transactions or a combination of certain transactions may result in material additional limitations on our ability to use our net operating loss and tax credit carryforwards.

Section 382 and 383 of the Internal Revenue Code of 1986, as amended, contain rules that limit the ability of a company that undergoes an ownership change, which is generally any change in ownership of more than 50% of its stock over a three-year period, to utilize its net operating loss and tax credit carryforwards and certain built-in losses recognized in years after the ownership change. These rules generally operate by focusing on ownership changes involving stockholders owning directly or indirectly 5% or more of the stock of a company and any change in ownership arising from a new issuance of stock by the company. Generally, if an ownership change occurs, the yearly taxable income limitation on the use of net operating loss and tax credit carryforwards and certain built-in losses is equal to the product of the applicable long term tax exempt rate and the value of the company’s stock immediately before the ownership change. We may be unable to offset our taxable income with losses, or our tax liability with credits, before such losses and credits expire and therefore would incur larger federal income tax liability. We have completed a number of financings since our inception which may have resulted in a change in control as defined by Section 382, or could result in a change in control in the future.

If we identify a material weakness in our internal control over financial reporting, our ability to meet our reporting obligations and the trading price of our stock could be negatively affected.

A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of our annual or interim

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financial statements will not be prevented or detected on a timely basis. Accordingly, a material weakness increases the risk that the financial information we report contains material errors.

We regularly review and update our internal controls, disclosure controls and procedures, and corporate governance policies. In addition, we are required under the Sarbanes-Oxley Act of 2002 to report annually on our internal control over financial reporting. Any system of internal controls, however well designed and operated, is based in part on certain assumptions and can provide only reasonable, not absolute, assurances that the objectives of the system are met. For example, in 2012 we updated our internal controls to include our operations in Sweden. If we, or our independent registered public accounting firm, determine that our internal controls over financial reporting are not effective, or we discover areas that need improvement in the future, these shortcomings could have an adverse effect on our business and financial results, and the price of our common stock could be negatively affected.

If we cannot conclude that we have effective internal control over our financial reporting, or if our independent registered public accounting firm is unable to provide an unqualified opinion regarding the effectiveness of our internal control over financial reporting, investors could lose confidence in the reliability of our financial statements, which could lead to a decline in our stock price. Failure to comply with reporting requirements could also subject us to sanctions and/or investigations by the SEC, The NASDAQ Stock Market or other regulatory authorities.

Item 1B. UNRESOLVED STAFF COMMENTS

None.

Item 2. PROPERTIES

We currently lease and occupy approximately 56,000 square feet of space located in Waltham, Massachusetts which serves as our corporate headquarters. We also conduct manufacturing, research and development, marketing and administrative operations at this facility. This lease expires on May 31, 2023. In addition, we lease approximately 10,000 square feet of space at a second location in Waltham for expanded manufacturing and administrative operations. This lease expired on December 31, 2012 and we now rent on a month-to-month basis. We also lease four adjacent buildings in Lund, Sweden totaling approximately 45,000 square feet of space used primarily for manufacturing and administrative operations. The lease for three buildings totaling approximately 41,000 square feet expires on June 30, 2017 while the lease for the fourth building with approximately 4,000 square feet of space expires on September 30, 2019.

During the fiscal year ended December 31, 2012, we incurred total rental costs for all facilities of approximately $2,183,000.

Item 3. LEGAL PROCEEDINGS

From time to time, we may be subject to legal proceedings and claims in the ordinary course of business. We are not currently aware of any such proceedings or claims that we believe will have, individually or in the aggregate, a material adverse effect on our business, financial condition or results of operations.

Item 4. MINE SAFETY DISCLOSURES

Not applicable.

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PART II

Item 5. MARKET FOR REGISTRANT’S COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES

Market Information

Our common stock is traded on the Nasdaq Global Market under the symbol “RGEN.” The quarterly high and low sales prices for our common stock are shown in the following tables.

	Year Ended December 31, 2012
	High		Low
First Quarter	$	6.00	$	3.40
Second Quarter	$	7.29	$	3.72
Third Quarter	$	6.36	$	3.78
Fourth Quarter	$	6.80	$	4.90
	Nine Months Ended December 31, 2011
	High		Low
First Quarter	$	4.20	$	3.30
Second Quarter	$	3.78	$	3.17
Third Quarter	$	3.72	$	2.90

Stockholders and Dividends

As of February 19, 2013, there were approximately 601 stockholders of record of our common stock. We have not paid any dividends since our inception and do not intend to pay any dividends on our common stock in the foreseeable future. We anticipate that we will retain all earnings, if any, to support our operations. Any future determination as to the payment of dividends will be at the sole discretion of our Board of Directors and will depend on our financial condition, results of operations, capital requirements and other factors our Board of Directors deems relevant.

Equity Compensation Plan Information

See Part III, Item 12 for information regarding securities authorized for issuance under our equity compensation plans.

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Issuer Purchases of Equity Securities

In June 2008, the Board of Directors authorized a program to repurchase up to 1.25 million shares of our common stock to be repurchased at the discretion of management from time to time in the open market or through privately negotiated transactions. The repurchase program has no set expiration date and may be suspended or discontinued at any time. We did not repurchase any shares of common stock during the year ended December 31, 2012. In prior years, we repurchased a total of 592,827 shares, leaving 657,173 shares remaining under this authorization.

The information contained in the performance graph shall not be deemed to be “soliciting material” or to be “filed” with the Securities and Exchange Commission, and such information shall not be incorporated by reference into any future filing under the Securities Act or Exchange Act, except to the extent that Repligen specifically incorporates it by reference into such filing.

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Item 6. SELECTED CONSOLIDATED FINANCIAL DATA

The following selected consolidated financial data are derived from the audited financial statements of Repligen, except for the consolidated financial data at December 31, 2010 and for the nine months then ended which are derived from unaudited financial statements. The selected financial data set forth below should be read in conjunction with our financial statements and the related notes thereto and “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included elsewhere in this Annual Report, our Transition Report on Form 10-K for the nine months ended December 31, 2011 and our Annual Reports on Form 10-K for the fiscal years ended March 31, 2011, and 2010.

	Year Ended December  31,			Nine Months  Ended December 31,						Years Ended March 31,
	2012			2011			2010			2011			2010			2009
	(In thousands except per share amounts)
Revenue:
Product revenue	$	41,834		$	13,215		$	11,811		$	14,961		$	10,305		$	14,529
Royalty and other revenue		20,433			10,235			9,574			12,330			10,666			14,833
Total revenue		62,267			23,450			21,385			27,291			20,971			29,362
Operating expenses:
Cost of product revenue		24,957			5,157			4,187			5,580			4,159			5,686
Cost of royalty and other revenue		2,213			1,315			1,161			1,537			1,347			1,091
Research and development		10,490			9,462			8,745			12,529			14,160			12,772
Selling, general and administrative		13,227			9,050			5,580			8,019			7,072			5,933
Contingent consideration – fair value adjustments		611			—			—			—			—			—
Gain on bargain purchase		(314	)		(427	)		—			—			—			—
Total operating expenses		51,184			24,557			19,673			27,665			26,738			25,482
Income (loss) from operations		11,083			(1,107	)		1,712			(374	)		(5,767	)		3,880
Investment income		219			161			287			357			870			1,896
Interest expense		(57	)		(28	)		(12	)		(26	)		(2	)		(3	)
Other income (expense)		26			(623	)		—			—			—			—
Income (loss) before income taxes		11,271			(1,597	)		1,987			(43	)		(4,899	)		5,773
Income tax (benefit) provision		(2,885	)		16			—			—			(835	)		27
Net income (loss)	$	14,156		$	(1,613	)	$	1,987		$	(43	)	$	(4,064	)	$	5,746
Earnings (loss) per share:
Basic	$	0.46		$	(0.05	)	$	0.06		$	(0.00	)	$	(0.13	)	$	0.19
Diluted	$	0.45		$	(0.05	)	$	0.06		$	(0.00	)	$	(0.13	)	$	0.18
Weighted average shares outstanding:
Basic		30,914			30,774			30,778			30,782			30,752			30,958
Diluted		31,253			30,774			30,949			30,782			30,752			31,290
	As of December 31,									As of March 31,
	2012			2011			2010			2011			2010			2009
	(In thousands)
Balance Sheet Data:
Cash and marketable securities (1)	$	49,970		$	36,025		$	60,285		$	61,503		$	59,146		$	63,961
Working capital		55,457			39,431			55,563			51,221			55,024			50,235
Total assets		97,010			76,057			73,099			72,294			71,420			73,755
Long-term obligations		2,133			2,606			617			584			642			82
Accumulated deficit		(105,151	)		(119,307	)		(115,934	)		(117,965	)		(117,921	)		(113,857	)
Stockholders’ equity		84,125			65,987			68,882			67,087			66,120			69,123

(1) Excludes restricted cash of $200 related to our headquarters’ lease arrangement for all years presented.

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Item 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

This Annual Report on Form 10-K contains forward-looking statements which are made pursuant to the safe harbor provisions of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). The forward-looking statements in this Annual Report on Form 10-K do not constitute guarantees of future performance. Investors are cautioned that statements in this Annual Report on Form 10-K that are not strictly historical statements, including, without limitation, statements regarding current or future financial performance, potential impairment of future earnings, management’s strategy, plans and objectives for future operations or acquisitions, product development and sales, clinical trials and results, litigation strategy, product candidate research, development and regulatory approval, selling, general and administrative expenditures, intellectual property, development and manufacturing plans, availability of materials and product and adequacy of capital resources and financing plans constitute forward-looking statements. Such forward-looking statements are subject to a number of risks and uncertainties that could cause actual results to differ materially from those anticipated, including, without limitation, the risks identified under the caption “Risk Factors” and other risks detailed in this Annual Report on Form 10-K and our other filings with the Securities and Exchange Commission. We assume no obligation to update any forward-looking information contained in this Annual Report on Form 10-K, except as required by law.

Overview

We are a life sciences company that develops, manufactures and markets high-value, consumable bioprocessing products for life sciences companies and biopharmaceutical manufacturing companies worldwide. We are a world-leading manufacturer of both native and recombinant forms of Protein A, critical reagents used in biomanufacturing to separate and purify monoclonal antibodies, a type of biologic drug. We also supply several growth factor products used to increase cell culture productivity during the biomanufacturing process. In the burgeoning area of disposable biomanufacturing technologies, we have developed and currently market a series of OPUS (Open-Platform, User-Specified) chromatography columns for use in clinical-scale manufacturing. These pre-packed, “plug-and-play” columns are uniquely flexible and customizable to our customers’ media and size requirements. We generally manufacture and sell Protein A and growth factors to life sciences companies under long-term supply agreements and sell our chromatography columns, as well as media and quality test kits, directly to biopharmaceutical companies or contract manufacturing organizations. We refer to these activities as our bioprocessing business.

On December, 20, 2011, we significantly increased the size of our bioprocessing business through a strategic acquisition. We acquired certain assets and assumed certain liabilities of Novozymes Biopharma Sweden, AB (“Novozymes”) in Lund, Sweden, including the manufacture and supply of cell culture ingredients and Protein A affinity ligands for use in industrial cell culture, stem and therapeutic cell culture and biopharmaceutical manufacturing (the “Novozymes Biopharma Business” and the acquisition of the Novozymes Biopharma Business, the “Novozymes Acquisition”) for a total upfront cash payment of 20.65 million Euros (~$26.9 million). As a result of the Novozymes Acquisition, we nearly doubled the size of our bioprocessing business.

Historically, Repligen also conducted activities aimed at developing proprietary therapeutic drug candidates, often with a potential of entering into a collaboration with a larger commercial stage pharmaceutical or biotechnology company in respect of these programs. In addition, we have out-licensed certain intellectual property to Bristol-Myers Squibb Company, or Bristol, from which we receive royalties on Bristol’s net sales in the United States of their product Orencia^®. As part of our strategic decision in 2012 to focus our efforts on our core bioprocessing business, we scaled back our efforts on our clinical development programs and increased our efforts to find collaboration partners to pursue the development and, if successful, commercialization of these drug programs. The current status of our development portfolio is:

• On December 28, 2012, we out-licensed our SMA program, led by RG3039, to Pfizer Inc., or Pfizer. Pursuant to this license agreement, Pfizer will assume the majority of the costs associated with

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completing the required clinical trials for this program as well as obtaining U.S. Food and Drug Administration (“FDA”) approval of the respective new drug application (“NDA”). Under the license agreement, we are obligated to conduct additional activities in support of this program, which will include completing the second cohort of the current Phase I trial and supporting the transition of the program to Pfizer. We expect to complete these activities in the first half of 2013.

• The most advanced product candidate in our development portfolio is RG1068, a synthetic human hormone being developed as a novel imaging agent for the improved detection of pancreatic duct abnormalities in combination with magnetic resonance imaging in patients with pancreatitis and potentially other pancreatic diseases. We submitted an NDA to the FDA and a marketing authorization application (“MAA”) to the European Medicines Agency (“EMA”) in the first quarter of 2012. In the second quarter of 2012, we received a complete response letter from the FDA, indicating the need for additional clinical efficacy and safety trial data. We are currently working with the FDA on the details of an additional Phase III trial. We believe providing certainty as to the requirements of this additional Phase III trial may be an important factor in the decision by third-parties that may wish to pursue a development or commercialization agreement with us for RG1068.

• Our third clinical development program was targeted at Friedrich’s Ataxia and led by RG2833, a class I histone deacetylase (“HDAC”) inhibitor. RG2833 has received Orphan Drug designation from the FDA and European Commission. We initiated a single, ascending dose Phase 1 study of RG2833 in Friedreich’s Ataxia patients in Italy in the fourth quarter of 2012 and expect to complete this trial in the first half of 2013. We believe the results of this trial may be an important consideration for any third-party that may wish to pursue a development or commercialization agreement with us for RG2833. We expect that any additional development activities that we may pursue in the future will be largely supported by sponsors or collaborators.

• On April 7, 2008, we entered into a settlement agreement with Bristol in connection with a patent infringement lawsuit we filed against Bristol. Under the terms of the agreement, Bristol is obligated to pay us royalties on its U.S. net sales of Orencia^® for any clinical indication at a rate of 1.8% for the first $500,000,000 of annual sales, 2.0% for the next $500,000,000 of annual sales and 4% of annual sales in excess of $1 billion. Under the terms of the agreement, we will not receive any future royalties on Bristol’s sales of Orencia^® made after December 31, 2013.

Total revenue for the fiscal year ended December 31, 2012 increased as compared to the nine-month fiscal year ended December 31, 2011 and is primarily due to the acquisition of the Novozymes business as well as increased royalty revenue from Bristol as their product Orencia^® continues to penetrate the market.

CRITICAL ACCOUNTING POLICIES AND ESTIMATES

While our significant accounting policies are more fully described in the notes to our financial statements, we have identified the policies and estimates below as being critical to our business operations and the understanding of our results of operations. The impact of and any associated risks related to these policies on our business operations are discussed throughout “Management’s Discussion and Analysis of Financial Condition,” including in the “Results of Operations” section, where such policies affect our reported and expected financial results.

Revenue recognition

Product Sales

We generate revenue from the sale of products, licensing transactions and research and development collaborations. Our product revenues are from the sale of bioprocessing products to customers in the life science and biopharmaceutical industries. We recognize revenue related to product sales upon delivery of the product to the customer as long as there is persuasive evidence of an arrangement, the sales price is fixed or determinable and collection of the related receivable is reasonably assured. Determination of whether these criteria have been

26

met are based on management’s judgments primarily regarding the fixed nature of the fee charged for the product delivered and the collectability of those fees. We have a few longstanding customers who comprise the majority of revenue and have excellent payment histories and therefore we do not require collateral. We have had no significant write-offs of uncollectible invoices in the periods presented.

At the time of sale, we also evaluate the need to accrue for warranty and sales returns. The supply agreements we have with our customers and related purchase orders identify the terms and conditions of each sale and the price of the goods ordered. Due to the nature of the sales arrangements, inventory produced for sale is tested for quality specifications prior to shipment. Since the product is manufactured to order and in compliance with required specifications prior to shipment, the likelihood of sales return, warranty or other issues is largely diminished. Sales returns and warranty issues are infrequent and have had nominal impact on our financial statements historically.

Orencia Royalty

In April 2008, we settled our outstanding litigation with Bristol and began recognizing royalty revenue from that settlement in fiscal year 2009 for Bristol’s net sales in the United States of Orencia^®, which is used in the treatment of rheumatoid arthritis. Pursuant to the settlement with Bristol, we recognized royalty revenue of $14,753,000 for the fiscal year ended December 31, 2012, $8,769,000 for the nine-month fiscal year ended December 31, 2011 and $10,251,000 for the fiscal year ended March 31, 2011. Revenue earned from Bristol royalties is recorded in the periods when it is earned based on royalty reports sent by Bristol to us. We have no continuing obligations to Bristol as a result of this settlement. Our royalty agreement with Bristol provides that we will receive such royalty payments on sales of Orencia^® by Bristol through December 31, 2013.

Pfizer License Agreement

In December 2012, we entered into an exclusive worldwide licensing agreement (the “License Agreement”) with Pfizer to advance the SMA program, which is led by RG3039 and also includes backup compounds and enabling technologies. Pursuant to the terms of the License Agreement, we received $5 million from Pfizer as an upfront payment on January 22, 2013 and are entitled to receive up to $65 million in potential future payments, a portion of which may be owed to third parties. These potential payments are approximately equally divided between milestones related to clinical development and initial commercial sales in specific geographies. In addition, we are entitled to receive royalties on any future sales of RG3039 or any SMA compounds developed under the License Agreement. The royalty rates are tiered and begin in the high single-digits for RG-3039 or lesser amounts for any backup compounds developed under the License Agreement. Our receipt of these royalties is subject to an obligation under an existing in-license agreement and other customary offsets and deductions. There are no refund provisions in this agreement.

Activities under this agreement were evaluated in accordance with ASC 605-25 to determine if they represented a multiple element revenue arrangement. We identified the following deliverables in the Pfizer agreement:

• An exclusive license to research, develop, manufacture, commercialize and use RG3039 and backup compounds for the treatment of SMA and other disorders (the “License”);

• Research and development services designed to transition the SMA program to Pfizer pursuant to a transition plan (the “Transition Services”) ;

• The completion of the second cohort of a phase I clinical trial that was underway at the time the License Agreement was signed; and

• An inventory of RG3039, that could be used in clinical development, specifically to complete the phase I clinical trial, referenced immediately above (the “Clinical Trial Material”).

Two criteria must be met in order for a deliverable to be considered a separate unit of accounting. The first criterion requires that the delivered item or items have value to the customer on a stand-alone basis. The second

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criterion, which relates to evaluating a general right of return, is not applicable because such a provision does not exist in the License Agreement. The deliverables outlined above were deemed to have stand-alone value and to meet the criteria to be accounted for as separate units of accounting. Factors considered in this determination included, among other things, whether any other vendors sell the items separately and if Pfizer could use the delivered item for its intended purpose without the receipt of the remaining deliverables. If multiple deliverables included in an arrangement are separable into different units of accounting, the multiple-element arrangements guidance addresses how to allocate the arrangement consideration to those units of accounting. The amount of allocable arrangement consideration is limited to amounts that are fixed or determinable. Arrangement consideration is allocated at the inception of the arrangement to the identified units of accounting based on their relative selling price.

We identified the arrangement consideration to allocate among the units of accounting as the $5.0 million non-refundable up-front payment and excluded the potential milestone payments provided for in the License Agreement from the arrangement consideration as they were not considered fixed or determinable at the time the License Agreement was signed. Because we had not sold these items on a standalone basis previously, we had no vendor-specific objective evidence of selling price. Furthermore, we did not have detailed third-party evidence of selling price, and as a result we used our best estimate of selling price for each item. In determining these prices, we considered what we would be willing to sell the items for on a standalone basis, what the market would bear for such items and what another party might charge for these items.

The up-front arrangement consideration allocated to the License was recognized upon delivery of the License as the risks and rewards associated with the License transferred at that time. We used a discounted cash flow analysis to determine the value of the license. Key assumptions in the analysis included: the estimated market size for a compound targeted at SMA, the estimated remaining costs of development and time to commercialization, and the probability of successfully developing and commercializing the program. Based on this analysis, we allocated $4,876,000 to the value of the license and recognized this amount as revenue in the fiscal year ended December 31, 2012.

The remaining $124,000 of value was allocated based on the following:

• The estimated selling price of the Transition Services was approximately $600,000 resulting in consideration allocation of approximately $76,000. We were able to derive a price for these services, in part because they are similar to services provided by a contract research organization. We based the selling price of the Transition Services on internal full-time equivalent personnel costs and external costs that we expect to incur to transition the program to Pfizer. We applied a mark-up on the internal full-time equivalent personnel costs consistent with that of contract research organizations.

• The estimated selling price of the completion of the second cohort of the clinical trial was approximately $275,000 resulting in consideration allocation of approximately $35,000. This estimated selling price is based on the estimated, remaining costs to complete this cohort. Since the costs are pursuant to an arrangement negotiated with a third-party clinical site, we believe that the external cost estimate included in the agreement represents the best estimate of selling price for this unit of accounting.

• The estimated selling price of the Clinical Trial Material was approximately $105,000 resulting in consideration allocation of approximately $13,000. The estimated selling price is based upon the cost of procuring such material from the contract manufacturing organization that made the material. Since these costs were incurred pursuant to an arrangement negotiated with a third-party contract manufacturing organization, we believes that the costs included in the agreement represents the best estimate of selling price for this unit of accounting.

We believe that a change in the key assumptions used to determine best estimate of selling price for each of the deliverables would not have a significant effect on the allocation of arrangement consideration.

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We intend to recognize the revenues related to the transfer of Clinical Trial Material upon transfer of title and risk of loss to Pfizer, which we expect to occur in the first half of 2013. We expect to recognize revenues related to the Transition Services and the completion of the second cohort ratably over the first six months of 2013.

Future milestone payments, if any, under the License Agreement will be recognized under the provisions of ASC 605-28, which was adopted by Repligen on January 1, 2011. ASC 605-28 allows an entity to make an accounting policy election to recognize a payment that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is considered an event if:

• It can only be achieved based in whole or in part on either (1) the Company’s performance or (2) on the occurrence of a specific outcome resulting from the Company’s performance;

• There is substantive uncertainty at the date an arrangement is entered into that the event will be achieved; and

• It would result in additional payments being due to the entity.

In addition to the $5 million up-front payment, we are also eligible to receive $65 million in potential milestone payments from Pfizer comprised of:

• Up to $30 million related to the achievement of specified clinical milestone events; and

• Up to $35 million related to the achievement of specified commercial sales events, specifically the first commercial sale in specific territories.

We believe that the $30 million of specified clinical milestone payments are substantive. We may receive all, or a portion of, the first clinical milestone of $2 million in 2013 depending upon the development path chosen by Pfizer. If we receive a portion of this milestone, we expect to receive the balance of it by the end of 2014.

Any milestones earned upon specified commercial sales events or future royalty payments, under the License Agreement will be recognized as revenue when they are earned.

Research and Development Agreements

In the fiscal year ended December 31, 2012, we also recognized $803,000 of revenue from sponsored research and development projects under agreements with the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, GoFar, and the Friedreich’s Ataxia Research Alliance. For the nine-month fiscal year ended December 31, 2011, we recognized approximately $1,466,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, Go Friedreich’s Ataxia Research (“GoFar”), and the Friedreich’s Ataxia Research Alliance. For the nine months ended December 31, 2010, we recognized $1,102,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. During the fiscal year ended March 31, 2011, we recognized approximately $1,346,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. In the fiscal year ended March 31, 2011, we also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

Research revenue is recognized when the expense has been incurred and services have been performed. Determination of which incurred costs qualify for reimbursement under the terms of our contractual agreements

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and the timing of when such costs were incurred involves the judgment of management. Our calculations are based upon the agreed-upon terms as stated in the arrangements. However, should the estimated calculations change or be challenged by other parties to the agreements, research revenue may be adjusted in subsequent periods. The calculations have not historically changed or been challenged, and we do not anticipate any significant subsequent change in revenue related to sponsored research and development projects.

There have been no material changes to our initial estimates related to revenue recognition in any periods presented in the accompanying consolidated financial statements.

Inventories

Inventories relate to our bioprocessing business. We value inventory at cost or, if lower, fair market value, using the first-in, first-out method. We review our inventory at least quarterly and record a provision for excess and obsolete inventory based on our estimates of expected sales volume, production capacity and expiration dates of raw materials, work-in-process and finished products. Expected sales volumes are determined based on supply forecasts provided by key customers for the next three to 12 months. We write down inventory that has become obsolete, inventory that has a cost basis in excess of its expected net realizable value, and inventory in excess of expected requirements to cost of product revenue. Manufacturing of bioprocessing finished goods is done to order and tested for quality specifications prior to shipment.

A change in the estimated timing or amount of demand for our products could result in additional provisions for excess inventory quantities on hand. Any significant unanticipated changes in demand or unexpected quality failures could have a significant impact on the value of inventory and reported operating results. During all periods presented in the accompanying consolidated financial statements, there have been no material adjustments related to a revised estimate of inventory valuations.

Business combinations

Amounts paid for acquisitions are allocated to the assets acquired and liabilities assumed, if any, based on their fair values at the dates of acquisition. The fair value of identifiable intangible assets is based on detailed valuations that use information and assumptions determined by management. Any excess of purchase price over the fair value of the net tangible and intangible assets acquired is allocated to goodwill. The fair value of contingent consideration includes estimates and judgments made by management regarding the probability that future contingent payments will be made, the extent of royalties to be earned in excess of the defined minimum royalties, etc. Management updates these estimates and the related fair value of contingent consideration at each reporting period. Changes in the fair value of contingent consideration are recorded in our Statement of Operations.

We use the income approach to determine the fair value of certain identifiable intangible assets including customer relationships and developed technology. This approach determines fair value by estimating after-tax cash flows attributable to these assets over their respective useful lives and then discounting these after-tax cash flows back to a present value. We base our assumptions on estimates of future cash flows, expected growth rates, expected trends in technology, etc. We base the discount rates used to arrive at a present value as of the date of acquisition on the time value of money and certain industry-specific risk factors. We believe the estimated purchased customer relationships and developed technology amounts so determined represent the fair value at the date of acquisition and do not exceed the amount a third party would pay for the assets.

Intangible assets and goodwill

Intangible Assets

We amortize our intangible assets that have finite lives using the straight-line method. Amortization is recorded over the estimated useful lives ranging from 8 to 8.5 years. We review our intangible assets subject to

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amortization to determine if any adverse conditions exist or a change in circumstances has occurred that would indicate impairment or a change in the remaining useful life. If the carrying value of an asset exceeds its undiscounted cash flows, we will write-down the carrying value of the intangible asset to its fair value in the period identified. In assessing fair value, we must make assumptions regarding estimated future cash flows and discount rates. If these estimates or related assumptions change in the future, we may be required to record impairment charges. We generally calculate fair value as the present value of estimated future cash flows to be generated by the asset using a risk-adjusted discount rate. If the estimate of an intangible asset’s remaining useful life is changed, we will amortize the remaining carrying value of the intangible asset prospectively over the revised remaining useful life.

Goodwill

We test goodwill for impairment on an annual basis and between annual tests if events and circumstances indicate it is more likely than not that the fair value of a reporting unit is less than its carrying value. Events that would indicate impairment and trigger an interim impairment assessment include, but are not limited to current economic and market conditions, including a decline in market capitalization, a significant adverse change in legal factors, business climate or operational performance of the business, and an adverse action or assessment by a regulator. Our annual impairment test date is the last day of our fiscal fourth quarter. For the fiscal year ended December 31, 2012, the impairment test date was December 31, 2012.

Accrued liabilities

We estimate accrued liabilities by identifying services performed on our behalf, estimating the level of service performed and determining the associated cost incurred for such service as of each balance sheet date. Examples of estimated accrued expenses include:

• Fees paid to contract manufacturers in conjunction with the production of clinical materials. These expenses are normally determined through a contract or purchase order issued by us;

• Service fees paid to organizations for their performance in conducting clinical trials. These expenses are determined by contracts in place for those services and communications with project managers on costs that have been incurred as of each reporting date; and

• Professional and consulting fees incurred with law firms, audit and accounting service providers and other third party consultants. These expenses are determined by either requesting those service providers to estimate unbilled services at each reporting date for services incurred or tracking costs incurred by service providers under fixed fee arrangements.

We have processes in place to estimate the appropriate amounts to record for accrued liabilities, which principally involve the applicable personnel reviewing the services provided. In the event that we do not identify certain costs that have begun to be incurred or we under or over-estimate the level of services performed or the costs of such services, the reported expenses for that period may be too low or too high. The date on which certain services commence, the level of services performed on or before a given date, and the cost of such services often require the exercise of judgment. We make these judgments based upon the facts and circumstances known at the date of the financial statements.

A change in the estimated cost or volume of services provided could result in additional accrued liabilities. Any significant unanticipated changes in such estimates could have a significant impact on our accrued liabilities and reported operating results. There have been no material adjustments to our accrued liabilities in any of the periods presented in the accompanying financial statements.

Stock-based compensation

We use the Black-Scholes option pricing model to calculate the fair value of share-based awards on the grant date.

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The expected term of options granted represents the period of time for which the options are expected to be outstanding and is derived from our historical stock option exercise experience and option expiration data. Accordingly, the expected term is presumed to be the midpoint between the vesting date and the end of the contractual term. In addition, for purposes of estimating the expected term, we have aggregated all individual option awards into one group as we do not expect substantial differences in exercise behavior among our employees. The expected volatility is a measure of the amount by which our stock price is expected to fluctuate during the expected term of options granted. We determined the expected volatility based upon the historical volatility of our common stock over a period commensurate with the option’s expected term, exclusive of any events not reasonably anticipated to recur over the option’s expected term. The risk-free interest rate is the implied yield available on U.S. Treasury zero-coupon issues with a remaining term equal to the option’s expected term on the grant date. We have never declared or paid any cash dividends on any of our capital stock and do not expect to do so in the foreseeable future. Accordingly, we use an expected dividend yield of zero to calculate the grant-date fair value of a stock option.

We recognize compensation expense on a straight-line basis over the requisite service period based upon options that are ultimately expected to vest, and accordingly, such compensation expense has been adjusted by an amount of estimated forfeitures. Forfeitures represent only the unvested portion of a surrendered option. Forfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Based on an analysis of historical data, we have calculated an 8% annual forfeiture rate for non-executive level employees, a 3% annual forfeiture rate for executive level employees, and a 0% forfeiture rate for non-employee members of the Board of Directors, which we believe is a reasonable assumption to estimate forfeitures. However, the estimation of forfeitures requires significant judgment and, to the extent actual results or updated estimates differ from our current estimates, such amounts will be recorded as a cumulative adjustment in the period estimates are revised.

For the fiscal year ended December 31, 2012, we recorded stock-based compensation expense of approximately $1,024,000. For the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, we recorded stock-based compensation expense of approximately $730,000 and $748,000, respectively, for stock options granted under the Second Amended and Restated 2001 Repligen Corporation Stock Plan (the “2001 Plan”). For the fiscal year ended March 31, 2011, we recorded stock-based compensation expense of approximately $1,003,000 for stock options granted under the 2001 Plan.

As of December 31, 2012, there was $1,605,995 of total unrecognized compensation cost related to unvested share-based awards. This cost is expected to be recognized over a weighted average remaining requisite service period of 2.76 years. We expect 739,009 unvested options to vest over the next five years.

Income Taxes

As of September 30, 2012, our U.S. net operating losses (“NOL’s”) and other deferred tax assets were fully offset by a valuation allowance primarily because we were in a cumulative loss position and did not have sufficient history of income to conclude that it was more likely than not that we would be able to realize the tax benefits of those deferred tax assets. In the fourth quarter of 2012, we entered into a three-year cumulative pre-tax income position and concluded that it was more likely than not that we will generate sufficient taxable income in 2013 based on our 2013 projections to realize the tax benefit of a portion of our deferred tax assets. As such, we reversed $3,021,000 of the deferred tax asset valuation allowance in the U.S in the fourth quarter of 2012. The amount is recorded as a benefit for income taxes in the consolidated statement of operations. As a result of the fact that we will no longer receive royalty payments on Bristol’s sales of Orencia after December 31, 2013, we concluded that realization of deferred tax assets beyond December 31, 2003 is not more likely than not, and as such, we continue to maintain a valuation allowance against those deferred tax assets estimated to reverse beyond 2013.

In supporting our conclusion that it was more likely than not that we would realize the tax benefits of certain of our deferred tax assets, we weighed the positive and negative evidence. The positive evidence included that

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fact that we had entered into a cumulative three-year pre-tax income position in the U.S. and were projecting significant pre-tax income in the U.S. in the year ending December 31, 2013, we have a history of operating within our projections, and the fact that a significant portion of our bioprocessing revenue and royalty payments on U.S. sales of Orencia are reasonably predictable due to our long-term supply agreements with certain customers and the fact that U.S. sales of Orencia have been increasing on a quarterly basis for several years. Our 2013 projections include estimates and assumptions as it relates to projected revenues and costs to be incurred. We believe that our projections are reasonable and supportable. Our projections also reflect significant planned reductions in research and development expenses associated with our therapeutic product candidates, as discussed elsewhere in this Form 10-K. We believe that this positive evidence outweighs the negative evidence, which included that fact that we were in a three-year cumulative loss position prior to the fourth quarter of 2012 and the fact that our projections for the year ending December 31, 2014 and beyond are significantly impacted by the fact that after December 31, 2013 we no longer receive royalty payments from Bristol on U.S. sales of Orencia.

RESULTS OF OPERATIONS

On December 15, 2011, we changed our fiscal year end from March 31 to December 31. As a result of this change, we filed a Transition Report on Form 10-K covering the nine-month transition period ending December 31, 2011. As a result of this change, “Fiscal 2012” refers to the twelve month period from January 1, 2012 through December 31, 2012. “Fiscal 2011” refers to the nine-month transition period from April 1, 2011 through December 31, 2011. “Fiscal 2010” refers to the unaudited nine-month period from April 1, 2010 through December 31, 2010.

The following discussion of the financial condition and results of operations should be read in conjunction with the accompanying consolidated financial statements and the related footnotes thereto.

Revenues

Total revenues for fiscal years 2012, 2011 and 2010 were comprised of the following:

	Year ended December 31,				Nine months  ended December 31,		% Change
	2012		2011		2010 (unaudited)		2012 vs. 2011			2011 vs. 2010
	(in thousands, except percentages)
Bioprocessing product revenue	$	41,834	$	13,215	$	11,811		217	%		12	%
Royalty and other revenue		20,433		10,235		9,574		100	%		7	%
Total revenue	$	62,267	$	23,450	$	21,385		166	%		10	%

Substantially all of our bioprocessing products are based on recombinant Protein A and are sold to customers who incorporate our manufactured products into their proprietary antibody purification systems to be sold directly to the pharmaceutical industry. Monoclonal antibodies are a well-established class of drug with applications in rheumatoid arthritis, asthma and a variety of cancers. Sales of our bioprocessing products are therefore impacted by the timing of large-scale production orders and the regulatory approvals for such antibodies, which may result in significant quarterly fluctuations.

For fiscal 2012, bioprocessing product sales increased by $28,619,000 or 217% as compared to fiscal 2011 driven predominantly by the acquisition of the Novozymes business which contributed $23,425,000 in revenue, the longer fiscal period in fiscal 2012 and increased demand from certain key customers. We sell our assorted bioprocessing products at various price points. The mix of products sold varies and impacts the fluctuations in total product revenue and cost of product revenues from period to period.

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For fiscal 2011, bioprocessing product sales increased by $1,404,000 or 12% as compared to fiscal 2010. Volume increased 14% due to increased demand from certain key customers and other business events, and was offset by a 2% decrease in sales revenue due to changes in the mix of products sold in fiscal 2011 as compared to fiscal 2010.

Pursuant to the settlement with Bristol, we recognized royalty revenue of $14,753,000 for fiscal 2012 as well as $8,769,000 and $7,739,000 for fiscal 2011 and 2010, respectively. For the year ending December 31, 2013, we expect royalty revenues to increase moderately over the prior year as Bristol’s Orencia^® continues to penetrate the market. The royalty arrangement with Bristol expires on December 31, 2013.

For fiscal 2012, we recognized $4,876,000 of revenue from the out-license of our Spinal Muscular Atrophy program to Pfizer on December 28, 2012. In fiscal 2012, we also recognized $803,000 of revenue from sponsored research and development projects under agreements with the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, GoFar, and the Friedreich’s Ataxia Research Alliance. For fiscal 2011, we recognized approximately $1,466,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, GoFar, and the Friedreich’s Ataxia Research Alliance. For fiscal 2010, we recognized $1,102,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance.

Following the out-license of the Spinal Muscular Atrophy program to Pfizer in December 2012, we expect research and license revenues to decrease in the year ending December 31, 2013 unless we are successful in out-licensing or receiving incremental funding for RG1068 or RG2833.

Costs and operating expenses

Total costs and operating expenses for fiscal years 2012, 2011 and 2010 were comprised of the following:

	Year ended December 31,						Nine months  ended December 31,		% Change
	2012			2011			2010 (unaudited)		2012 vs. 2011			2011 vs. 2010
	(in thousands, except percentages)
Cost of product revenue	$	24,957		$	5,157		$	4,187		384	%		23	%
Cost of royalty and other revenue		2,213			1,315			1,161		68	%		13	%
Research and development		10,490			9,462			8,745		11	%		8	%
Selling, general and administrative		13,227			9,050			5,580		46	%		62	%
Contingent consideration – fair value adjustments		611			—			—		100	%		—
Gain on bargain purchase		(314	)		(427	)		—		26	%		—
Total costs and operating expenses	$	51,184		$	24,557		$	19,673		108	%		25	%

For fiscal 2012, cost of product revenue increased $19,800,000 or 384% as compared to fiscal 2011. This increase is primarily due to a 217% increase in bioprocessing product sales driven by the Novozymes acquisition and overall higher production costs at our newly acquired Sweden facility.

For fiscal 2011, cost of product revenue increased $970,000 or 23% as compared to fiscal 2010. This increase is primarily due to a 12% increase in bioprocessing product sales as well as the addition of the Novozymes Biopharma Business which accounts for $76,000 of the cost of product revenue increase.

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Gross margins were 40%, 61% and 65% for fiscal 2012, 2011 and 2010, respectively. During the current year, the Company began an extensive cost reduction initiative of both the Sweden and Waltham facilities. As a result of these efforts, we anticipate that gross margins will improve in the year ending December 31, 2013.

Pursuant to the settlement with Bristol, we must remit 15% of royalty revenue received through the expiration of the agreement in December 2013 to the University of Michigan. For the fiscal years 2012, 2011 and 2010, cost of royalty revenue was $2,213,000, $1,315,000 and $1,161,000, respectively. These increases are directly related to the increases in Bristol royalty revenues noted above.

Research and development costs represent bioprocessing product and therapeutic drug development and primarily include costs of internal personnel, supplies, external pharmacology and toxicology research, clinical trials and the costs associated with the manufacturing and testing of clinical materials. In August, 2012, we announced a strategic focus on our Bioprocessing business and a simultaneous effort to find partners, out-licensing opportunities or other funding arrangements with external parties to reduce or eliminate the net expenditures on research and development activities for our therapeutic programs. Those efforts are ongoing. In December 2012, we announced that we entered into an outlicensing agreement with Pfizer, Inc. for our Spinal Muscular Atrophy program, under an arrangement that would provide $5.0 million up front and up to $65.0 million in future milestones, plus royalties.

In June 2012, we received a complete response letter from the NDA on our NDA for SecreFlo for pancreatic imaging indicating that additional clinical data would be required to support potential approval in the United States. We simultaneously withdrew our MAA for SecreFlo from consideration by the EMA. We believe that SecreFlo, if approved, would provide a safe and effective means to non-invasively image the pancreas with MRI and will meet an important unmet medical need for patients with pancreatitis. However, given the shift in strategic focus towards Bioprocessing product sales, we are seeking partners to either out-license or fund the development of this program and as such do not anticipate incurring material expenditures under this program without entering into such arrangements.

In addition, we are performing Phase 1 clinical study of RG2833 in patients with Friedreich’s ataxia. We receive funding from a number of sponsors on this program that significantly mitigates the net expense of the programs and we are pursuing the clinical trial and other key program objectives that will enable the recognition of revenues under these sponsored research agreements and with the goal of making the program more viable from a partnering or out-licensing perspective.

Due to the small size of the Company and the fact that these various programs share personnel and fixed costs, we do not track all of our expenses or allocate any fixed costs by program, and therefore, have not provided an estimate of historical costs incurred by project.

Each of our therapeutic research and development programs is subject to risks and uncertainties, including the requirement to seek regulatory approvals that are outside of our control. For example, our clinical trials may be subject to delays based on our inability to enroll patients at the rate that we expect to meet the schedule for our planned clinical trials. Moreover, the product candidates identified in these research programs, particularly in our early stage programs must overcome significant technological, manufacturing and marketing challenges before they can be successfully commercialized. For example, results from our preclinical animal models may not be replicated in our clinical trials with humans. As a result of these risks and uncertainties, we are unable to predict with any certainty the period in which material net cash inflows from such projects could be expected to commence or the completion dates of these programs.

These risks and uncertainties generally prevent us from estimating with any certainty the specific timing and future costs of our research and development programs, although historical trends within the industry suggest that gross expenses tend to increase in later stages of development. As mentioned above, however, we anticipate entering into partnering, outlicensing or other such arrangements in the coming year, similar to the Pfizer license,

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in order to fund those gross expenditures. Arrangements with commercial vendors and academic researchers accounted for 30%, 47% and 51% of our research and development expenses for fiscal 2012, 2011 and 2010, respectively. The outsourcing of such services provides us flexibility to discontinue or increase spending depending on the success of our research and development programs.

For fiscal 2012, research and development expenses increased by $1,028,000 or 11% as compared to fiscal 2011. This increase is comprised primarily of a $551,000 increase in bioprocessing process development costs due to the Novozymes acquisition and $245,000 of severance and related expenses associated with the shift towards bioprocessing and a longer fiscal period in 2012 versus 2011.

For fiscal 2011, research and development expenses increased by $718,000 or 8% as compared to fiscal 2010. This increase is comprised primarily of (1) a $1,939,000 increase in costs associated with drug product manufacturing and other costs associated with the NDA submission for SecreFlo for MRI imaging of the pancreas, offset by a $500,000 settlement related to this program from a dispute with Parexel International Corporation, the parent company of Perceptive Informatics, Inc. and (2) a $765,000 increase related to RG3039 for spinal muscular atrophy, which includes a $500,000 milestone payment made in April 2011 upon successful filing of our Investigational New Drug Application with the FDA, as well as other costs associated with the initiation of our Phase 1 clinical trial. These increases were partially offset by a $1,344,000 decrease related to RG2417 for the treatment of patients with bipolar disorder as we discontinued this program in March 2011 and a $603,000 decrease related to our Friedreich’s ataxia program as we incurred higher costs in the prior period related to testing and drug substance manufacture in preparation for our upcoming Phase 1 study of RG2833 in adult patients with Friedreich’s ataxia in Europe.

Future research and development expenses are dependent on a number of variables, including the cost and design of clinical trials and external costs such as manufacturing of clinical materials as well as the availability of external funding to support those programs. We expect our research and development expenses in the year ending December 31, 2013 to decrease significantly now that the Spinal Muscular Atrophy program was licensed to Pfizer and we focus our therapeutics efforts on finding partners to fund or out-license the SecreFlo and Friedreich’s Ataxia programs.

Selling, general and administrative (“SG&A”) expenses include the costs associated with selling our commercial products and costs required to support our research and development efforts, including legal, accounting, patent, shareholder services, amortization of intangible assets and other administrative functions. In addition, SG&A expenses have historically included costs associated with various litigation matters.

For fiscal 2012, SG&A costs increased by $4,177,000 or 46% as compared to fiscal 2011. This increase is primarily comprised of an incremental $1,500,000 in SG&A from our newly acquired Swedish subsidiary, approximately $2,400,000 which represents an additional quarter of our traditional U.S. operations as fiscal 2012 was a longer fiscal period than fiscal 2011, and other miscellaneous expenses.

For fiscal 2011, SG&A costs increased by $3,470,000 or 62% as compared to fiscal 2010. This increase is primarily comprised of approximately $1,700,000 in transaction costs related to the Novozymes Acquisition, $380,000 related to commercialization efforts as we prepared to launch SecreFlo for MRI imaging of the pancreas, pending FDA approval, $420,000 due to headcount increases in marketing and business development, including salaries, stock-based compensation and recruiting costs, $410,000 related to business development activities, and $200,000 due to increased development and sales and marketing activities related to our OPUS product.

We expect SG&A expenses to decrease slightly in the year ending December 31, 2013 primarily because we do not expect a recurrence of the deal costs associated with the Novozymes Acquisition that we incurred in 2012. In addition, the prior year included certain marketing research expenditures associated with the anticipated approval of SecreFlo that have been eliminated going forward upon receipt of the complete response letter.

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For fiscal 2012 and 2011, we recorded a $314,000 and $427,000 gain on bargain purchase, respectively, related to the Novozymes Acquisition on December 20, 2011.

Investment income

Investment income includes income earned on invested cash balances. Investment income for fiscal 2012, 2011 and 2010 was $219,000, $161,000 and $287,000, respectively. The increase of $58,000 or 36% for fiscal 2012 compared to fiscal 2011 was due to slightly higher interest rates after an unusually low fiscal 2011 and a longer period in fiscal 2012. The decrease of $126,000 or 44% for fiscal 2011 compared to fiscal 2010 was primarily attributable to lower interest rates and a shorter period in fiscal 2011. We expect interest income to vary based on changes in the amount of funds invested and fluctuation of interest rates.

(Benefit from) provision for income taxes

In the year ended December 31, 2012, we recorded a tax benefit of $2,885,000 that is comprised of the reversal of $3,021,000 of the valuation allowance on our deferred tax assets offset by a provision for a state tax liability. In the fourth quarter of 2012, we entered into a cumulative pre-tax income position and concluded that it was more likely than not that we will generate sufficient taxable income in 2013 based on our 2013 projections to realize the tax benefit of a portion of our deferred tax assets.

In the nine-month fiscal year ended December 31, 2011, we recorded a tax provision of $16,000 that is comprised of a $48,000 provision for a deferred tax liability related to goodwill amortization and a $32,000 benefit for a deferred tax asset related to a net operating loss for Repligen Sweden AB.

Liquidity and capital resources

We have financed our operations primarily through sales of equity securities, revenues derived from product sales, and research grants, as well as proceeds and royalties from license arrangements and a litigation settlement. Our revenue for the foreseeable future will be limited to our bioprocessing product revenue, royalties from Bristol’s sales of Orencia^® through December 31, 2013, and research and development grants. Given the uncertainties related to pharmaceutical product development, we are currently unable to reliably estimate when, if ever, our therapeutic product candidates will generate revenue and cash flows.

At December 31, 2012, we had cash and marketable securities of $49,970,000 compared to $36,025,000 at December 31, 2011. A deposit for leased office space of $200,000 is classified as restricted cash and is not included in cash and marketable securities total for December 31, 2012 or December 31, 2011.

Cash flows

(In thousands)
Cash provided by (used in)	Year ended December 31, 2012		Increase / (Decrease)		Nine months ended December 31, 2011			Increase / (Decrease)			Nine months ended December 31, 2010 (unaudited)
Operating activities	$	13,440	$	11,127	$	2,311		$	523		$	1,788
Investing activities		2,841		7,852		(5,011	)		(523	)		(4,488	)
Financing activities		1,159		1,490		(331	)		(300	)		(31	)

Operating activities

For fiscal 2012, our operating activities provided cash of $13,440,000 reflecting net income of $14,156,000 and non-cash charges totaling $2,383,000 including depreciation, amortization, stock-based compensation

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charges, deferred tax asset valuation allowance changes, the revaluation of contingent consideration and the gain on bargain purchase. Decreases in inventory and increases in accounts payable and accrued liabilities provided an additional $2,734,000 and $3,086,000 of cash. These increases were offset by an increase of $5,924,000 in royalties and other receivables associated primarily with the up-front payment pursuant to the Pfizer license agreement.

For fiscal 2011, our operating activities provided cash of $2,311,000 reflecting a net loss of $1,613,000 and non-cash charges totaling $1,624,000 including depreciation, amortization, stock-based compensation charges and the gain on bargain purchase. The remaining cash flow provided in operations resulted from favorable changes in various working capital accounts. For fiscal 2010, our operating activities provided cash of $1,788,000 reflecting net income of $1,987,000 and non-cash charges totaling $2,022,000 including depreciation, amortization, and stock-based compensation charges. The remaining cash flow used in operations resulted from unfavorable changes in various working capital accounts.

Investing activities

We place our marketable security investments in high quality credit instruments as specified in our investment policy guidelines. For fiscal 2012, our investing activities provided $2,841,000 of cash, which is primarily capital expenditures of $1,264,000, offset by net redemptions of marketable securities of $4,105,000. For fiscal 2011, our investing activities consumed $5,011,000 of cash, which is primarily due to the Novozymes Acquisition for $26,884,000 and capital expenditures of $575,000, offset by net redemptions of marketable securities of $22,449,000. During fiscal 2010, our investing activities consumed $4,488,000 of cash, which is primarily due to $3,870,000 of net purchases of marketable securities, $318,000 of capital expenditures and a $300,000 milestone payment related to our acquisition of the assets of BioFlash. We expect capital expenditures to increase in 2013 and 2014 as compared to 2012 as we expand our Waltham facility.

Financing activities

Exercises of stock options provided cash receipts of $1,159,000 and $25,000 in fiscal 2012 and 2010, respectively. In 2011, there were no stock option exercises. During fiscal 2011, the repurchase of common stock consumed $331,000.

Off-balance sheet arrangements

We do not have any special purpose entities or off-balance sheet financing arrangements.

Contractual obligations

As of December 31, 2012, we had the following fixed obligations and commitments:

	Payments Due By Period
(In thousands)	Total		Less than 1 Year		1 – 3 Years		3 – 5 Years		More than 5 Years
Operating lease obligations	$	16,153	$	2,222	$	4,445	$	3,878	$	5,608
Purchase obligations (1)		2,872		2,872		—		—		—
Contingent consideration (2)		2,900		1,377		1,199		207		117
Total	$	21,925	$	6,471	$	5,644	$	4,085	$	5,725

(1) Primarily represents purchase orders for the procurement of raw material for manufacturing.

(2) These contingent consideration amounts relating to acquisitions are recorded in accrued expenses and long term liabilities on our consolidated balance sheets.

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Capital requirements

Our future capital requirements will depend on many factors, including the following:

• the expansion of our bioprocessing business;

• the ability to sustain sales and profits of our bioprocessing products;

• the resources required to successfully integrate the Novozymes Biopharma Business and recognize expected synergies;

• our ability to establish one or more partnerships for development and commercialization of RG1068 or our early stage CNS programs;

• the scope of and progress made in our research and development activities;

• our ability to acquire additional bioprocessing products or product candidates;

• the extent of any share repurchase activity;

• the success of any proposed financing efforts; and

• the amount of royalty revenues we receive from Bristol through December 31, 2013.

Absent acquisitions of additional products, product candidates or intellectual property, we believe our current cash balances are adequate to meet our cash needs for at least the next 24 months. We expect operating expenses in the year ending December 31, 2013 to decrease significantly as we invest less in therapeutic drug development and simultaneously improve gross margins through greater optimization of our two production facilities and other process improvements we have developed internally. We expect to incur continued spending related to the development and expansion of our bioprocessing product lines for the foreseeable future. Our future capital requirements may include, but are not limited to, expansion of our Waltham facility and other purchases of property, plant and equipment, the acquisition of additional bioprocessing products and technologies to complement our existing manufacturing capabilities, and continued investment in our intellectual property portfolio.

We plan to continue to invest in our bioprocessing business and in key research and development activities associated with our efforts to identify and consummate development and commercialization partnerships. We actively evaluate various strategic transactions on an ongoing basis, including monetizing existing assets and licensing or acquiring complementary products, technologies or businesses that would complement our existing portfolio of development programs. We continue to seek to acquire such potential assets that may offer us the best opportunity to create value for our shareholders. In order to acquire such assets, we may need to seek additional financing to fund these investments. This may require the issuance or sale of additional equity or debt securities. The sale of additional equity may result in additional dilution to our stockholders. Should we need to secure additional financing to acquire a product, fund future investment in research and development, or meet our future liquidity requirements, we may not be able to secure such financing, or obtain such financing on favorable terms because of the volatile nature of the biotechnology marketplace.

Net operating loss carryforwards

At December 31, 2012, we had net operating loss carryforwards of approximately $44,678,000 and business tax credits carryforwards of approximately $2,160,000 available to reduce future federal income taxes, if any. The net operating loss and business tax credits carryforwards will continue to expire at various dates through December 2031. Net operating loss carryforwards and available tax credits are subject to review and possible adjustment by the Internal Revenue Service and may be limited in the event of certain changes in the ownership interest of significant stockholders.

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Foreign earnings

At December 31, 2012, we have not provided for U.S. income taxes or foreign withholding taxes on outside basis differences of foreign subsidiaries of approximately $477,000 as we have the ability and intend to indefinitely reinvest the undistributed earnings of Repligen Sweden and there are no needs for such earnings in the U.S. that would contradict our plan to indefinitely reinvest.

Effects of inflation

Our assets are primarily monetary, consisting of cash, cash equivalents and marketable securities. Because of their liquidity, these assets are not directly affected by inflation. Since we intend to retain and continue to use our equipment, furniture and fixtures and leasehold improvements, we believe that the incremental inflation related to replacement costs of such items will not materially affect our operations. However, the rate of inflation affects our expenses, such as those for employee compensation and contract services, which could increase our level of expenses and the rate at which we use our resources.

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Item 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Interest rate risk

We have investments in commercial paper, U.S. Government and agency securities as well as corporate bonds and other debt securities. As a result, we are exposed to potential loss from market risks that may occur as a result of changes in interest rates, changes in credit quality of the issuer or otherwise.

We generally place our marketable security investments in high quality credit instruments, as specified in our investment policy guidelines. A hypothetical 100 basis point decrease in interest rates would result in an approximate $172,000 decrease in the fair value of our investments as of December 31, 2012. We believe, however, that the conservative nature of our investments mitigates our interest rate exposure, and our investment policy limits the amount of our credit exposure to any one issue, issuer (with the exception of U.S. agency obligations) and type of instrument. We do not expect any material loss from our marketable security investments and therefore believe that our potential interest rate exposure is limited.

Foreign exchange risk

Transactions by our subsidiary, Repligen Sweden, may be denominated in Swedish kronor, British pound sterling, U.S. dollars, or in Euros while the entity’s functional currency is the Swedish krona. Exchange gains or losses resulting from the translation between the transactional currency and the functional currency of Repligen Sweden are included in our consolidated statements of operations. The functional currency of the Company is U.S. dollars. Fluctuations in exchange rates may adversely affect our results of operations, financial position and cash flows. We currently do not seek to hedge this exposure to fluctuations in exchange rates.

Although a majority of our contracts are denominated in U.S. dollars, 28% and 0% of total revenues during fiscal 2012 and 2011, respectively, were denominated in foreign currencies while 39% and 1% of our costs and expenses during fiscal 2012 and 2011, respectively, were denominated in foreign currencies, primarily operating expenses associated with cost of revenue, sales and marketing and general and administrative. In addition, 37% and 38% of our consolidated tangible assets were subject to foreign currency exchange fluctuations as of each of December 31, 2012 and 2011, respectively, while 48% and 44% of our consolidated liabilities were exposed to foreign currency exchange fluctuations as of each of December 31, 2012 and 2011, respectively.

Item 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

Financial statements and supplementary data required by Item 8 are set forth at the pages indicated in Item 15(a) below and are incorporated herein by reference.

Item 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE.

None.

Item 9A. CONTROLS AND PROCEDURES

(a) Disclosure Controls and Procedures.

The Company’s management, with the participation of our principal executive officer and principal financial officer, has evaluated the effectiveness of the Company’s disclosure controls and procedures (as defined in Rules 13a-15(e) or 15d-15(e) under the Exchange Act and as required by paragraph (b) of Rules 13a-15 or 15d-15 under the Exchange Act) as of the end of the period covered by this report. Based on such evaluation, our principal executive officer and principal financial officer have concluded that, as of the end of such period, the Company’s disclosure controls and procedures were effective at the reasonable assurance level.

41

(b) Report of Management on Internal Control Over Financial Reporting.

Management of the Company is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is defined in Rule 13a-15(f) and 15d-15(f) under the Exchange Act as a process designed by, or under the supervision of, the Company’s principal executive and principal financial officers and effected by the Company’s Board of Directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with U.S. generally accepted accounting principles and includes those policies and procedures that:

• pertain to the maintenance of records that in reasonable detail accurately and fairly reflect the transactions and dispositions of the assets of the Company;

• provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the Company are being made only in accordance with authorizations of management and directors of the Company; and

• provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of the Company’s assets that could have a material effect on the financial statements.

Management assessed the effectiveness of the Company’s internal control over financial reporting as of December 31, 2012. In making this assessment, management used the criteria established in Internal Control—Integrated Framework, issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO).

Subject to the foregoing, based on this assessment, our management concluded that, as of December 31, 2012, our internal control over financial reporting is effective based on those criteria. Ernst & Young LLP, the independent registered public accounting firm that audited our financial statements included in this Annual Report on Form 10-K, has issued an attestation report on our internal control over financial reporting as of December 31, 2012.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Projections of any evaluation of effectiveness to future periods are subject to the risks that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

42

(c) Attestation Report of the Independent Registered Public Accounting Firm.

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

To the Board of Directors and Stockholders of Repligen Corporation:

We have audited Repligen Corporation’s (the “Company”) internal control over financial reporting as of December 31, 2012, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (the COSO criteria). Repligen Corporation’s management is responsible for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Report of Management on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the company’s internal control over financial reporting based on our audit.

We conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion.

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

In our opinion, Repligen Corporation maintained, in all material respects, effective internal control over financial reporting as of December 31, 2012, based on the COSO criteria.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), the consolidated balance sheets of Repligen Corporation as of December 31, 2012 and December 31, 2011, and the related consolidated statements of operations and comprehensive income (loss), stockholders’ equity, and cash flows for the year ended December 31, 2012, the nine months ended December, 31, 2011 and the year ended March 31, 2011 of Repligen Corporation and our report dated March 15, 2013 expressed an unqualified opinion thereon.

/s/ Ernst & Young LLP

Boston, Massachusetts

March 15, 2013

43

(d) Changes in Internal Control Over Financial Reporting.

There have not been any changes in the Company’s internal control over financial reporting (as such term is defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during the quarter ended December 31, 2012 that have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting.

Item 9B. OTHER INFORMATION

None.

44

PART III

Pursuant to General Instructions G to Form 10-K, the information required for Part III, Items 10, 11, 12, 13 and 14, is incorporated herein by reference from the Company’s proxy statement for the 2013 Annual Meeting of Stockholders.

45

PART IV

Item 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

The following documents are filed as part of this Annual Report on Form 10-K:

(a) (1) Financial Statements:

The financial statements required by this item are submitted in a separate section beginning on page 36 of this Report, as follows:

	Page
Report of Independent Registered Public Accounting Firm		55
Consolidated Balance Sheets as of December 31, 2012 and December 31, 2011		56
Consolidated Statements of Operations and Comprehensive Income (Loss) for the Year Ended December  31, 2012, the Nine Months Ended December 31, 2011 and 2010 (unaudited) and for the Year Ended March 31, 2011		57
Consolidated Statements of Stockholders’ Equity for the Year Ended December  31, 2012, the Nine Months Ended December 31, 2011 and for the Year Ended March 31, 2011		58
Consolidated Statements of Cash Flows for the Year Ended December  31, 2012, the Nine Months Ended December 31, 2011 and 2010 (unaudited) and for the Year Ended March 31, 2011		59
Notes to Consolidated Financial Statements		60

(a) (2) Financial Statement Schedules:

None.

46

(a) (3) Exhibits:

The Exhibits which are filed as part of this Annual Report or which are incorporated by reference are set forth in the Exhibit Index hereto.

EXHIBIT INDEX

Exhibit Number	Document Description
3.1	Restated Certificate of Incorporation dated June 30, 1992 and amended September 17, 1999 (filed as Exhibit 3.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 1999 and incorporated herein by reference) (SEC File No. 000-14656).
3.2	Amended and Restated Bylaws (filed as Exhibit 3.2 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2003 and incorporated herein by reference) (SEC File No. 000-14656).
3.3	Amendment No. 1 to the Amended and Restated Bylaws (filed as Exhibit 3.1 to Repligen Corporation’s Current Report on Form 8-K filed on December 20, 2011 and incorporated herein by reference).
3.4	Amendment No. 2 to the Amended and Restated Bylaws (filed as Exhibit 3.1 to Repligen Corporation’s Current Report on Form 8-K filed on May 25, 2012 and incorporated herein by reference).
4.1	Specimen Stock Certificate (filed as Exhibit 4.1 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.1*	Consulting Agreement, dated November 1, 1981, between Dr. Alexander Rich and Repligen Corporation. (filed as Exhibit 10.2 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.2*	Employment Agreement, dated March 14, 1996, between Repligen Corporation and Walter C. Herlihy (filed as Exhibit 10.3 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.3*	Employment Agreement, dated March 14, 1996, between Repligen Corporation and James R. Rusche (filed as Exhibit 10.4 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.4*	Employment Agreement, dated March 14, 1996, between Repligen Corporation and Daniel P. Witt (filed as Exhibit 10.5 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.5*	Employment Offer Letter dated February 29, 2008 by and between Repligen Corporation and William Kelly (filed as Exhibit 10.20 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2008 and incorporated herein by reference).
10.6*	Repligen Executive Incentive Compensation Plan (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on form 8-K filed on December 14, 2005 and incorporated herein by reference).
10.7*	The Amended 1992 Repligen Corporation Stock Option Plan, as amended (filed as Exhibit 4.2 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2000 and incorporated herein by reference) (SEC File No. 000-14656).
10.8*	The Second Amended and Restated 2001 Repligen Corporation Stock Plan (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on September 18, 2008 and incorporated herein by reference).

47

Exhibit Number	Document Description
10.8.1*	The Amended and Restated 2001 Repligen Corporation Stock Option Plan, Form of Incentive Stock Option Agreement (filed as Exhibit 10.14 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2005 and incorporated herein by reference).
10.8.2*	The Amended and Restated 2001 Repligen Corporation Stock Plan, Form of Restricted Stock Agreement (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on January 9, 2006 and incorporated herein by reference).
10.9	Common Stock Purchase Warrant dated April 6, 2007 (filed as Exhibit 4.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2007 and incorporated herein by reference).
10.10#	Manufacturing Transfer Agreement dated as of December 17, 1998 among the Company and Amersham Pharmacia Biotech AB (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended December 31, 1998 and incorporated herein by reference) (SEC File No. 000-14656).
10.11#	License Agreement dated as of July 24, 2000 with University of Michigan (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2000 and incorporated herein by reference) (SEC File No. 000-14656).
10.12	Lease Between Repligen Corporation as Tenant and West Seyon LLC as Landlord, 35 Seyon Street, Waltham, MA (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended December 31, 2001 and incorporated herein by reference) (SEC File No. 000-14656).
10.13#	License Agreement by and between The Scripps Research Institute and Repligen Corporation dated April 6, 2007 (filed as Exhibit 10.18 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2007 and incorporated herein by reference).
10.14#	Settlement and Release Agreement dated April 7, 2008 by and among Repligen Corporation, The Regents of the University of Michigan and Bristol-Myers Squibb Company (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2008 and incorporated herein by reference).
10.15#	Strategic Supplier Alliance Agreement dated January 28, 2010 by and between Repligen Corporation and GE Healthcare Bio-Sciences AB (filed as Exhibit 10.17 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2010 and incorporated herein by reference).
10.16	First Amendment to Lease, dated July 5, 2011, by and between Repligen Corporation and TC Saracen, LLC (filed as Exhibit 10.1 to Repligen’s Current Report on Form 8-K filed on July 5, 2011 and incorporated herein by reference).
10.17	Asset Transfer Agreement by and among Repligen Corporation, Repligen Sweden AB, Novozymes Biopharma DK A/S and Novozymes Biopharma Sweden AB, dated October 27, 2011 (filed as Exhibit 2.1 to Repligen Corporation’s Current Report on Form 8-K filed on October 28, 2011 and incorporated herein by reference).
10.18	Lease Between Repligen Sweden AB (as successor-in-interest to Novozymes Biopharma Sweden AB) as Tenant and i-parken i Lund AB as Landlord, St. Lars Vag 47, 220 09 Lund, Sweden (filed as Exhibit 10.18 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).
10.19#	Amendment No. 1 to Strategic Supplier Alliance Agreement, by and between GE Healthcare Bio-Sciences AB and Repligen Corporation, dated as of October 27, 2011 (filed as Exhibit 10.19 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).

48

Exhibit Number	Document Description
10.20#	Strategic Supplier Alliance Agreement – Contract Manufacturing, by and between GE Healthcare Bio-Sciences AB and Repligen Sweden AB (as successor-in-interest to Novozymes Biopharma Sweden AB), dated as of July 7, 2011 (filed as Exhibit 10.20 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).
10.21#	Amendment to Strategic Supply Alliance Agreement, by and between GE Healthcare Bio-Sciences AB and Repligen Sweden AB (as successor-in-interest to Novozymes Biopharma Sweden AB), dated as of October 27, 2011 (filed as Exhibit 10.21 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).
10.22*	Repligen Corporation 2012 Stock Option and Incentive Plan (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on May 25, 2012 and incorporated herein by reference).
10.23*	Repligen Corporation Non-Employee Directors’ Deferred Compensation Plan (filed as Exhibit 10.2 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2012 and incorporated herein by reference).
10.24*	Letter Agreement, dated as of September 20, 2012, by and between Repligen Corporation and Jonathan I. Lieber (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on September 21, 2012 and incorporated herein by reference).
10.25#+	License Agreement, dated as of December 28, 2012, by and between Pfizer Inc. and Repligen Corporation.
21.1+	Subsidiaries of the Registrant.
23.1+	Consent of Ernst & Young LLP.
24.1+	Power of Attorney (included on signature page).
31.1+	Rule 13a-14(a)/15d-14(a) Certification.
31.2+	Rule 13a-14(a)/15d-14(a) Certification.
32.1+	Certification Pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101^	The following materials from Repligen Corporation on Form 10-K for the fiscal year ended December 31, 2012, formatted in Extensive Business Reporting Language (XBRL): (i) Consolidated Statements of Operations, (ii) Consolidated Balance Sheets, (iii) Consolidated Statement of Stockholders’ Equity, (iv) Consolidated Statements of Cash Flows, and (v) Notes to Consolidated Financial Statements, tagged as blocks of text.

# Confidential treatment obtained as to certain portions.

* Management contract or compensatory plan or arrangement.

+ Filed herewith.

^ As provided in Rule 406T of Regulation S-T, the XBRL-related information in Exhibit 101 to this Form 10-K is furnished and not filed for purposes of Sections 11 and 12 of the Securities Act of 1933 and Section 18 of the Securities Exchange Act of 1934.

The exhibits listed above are not contained in the copy of the Annual Report on Form 10-K distributed to stockholders. Upon the request of any stockholder entitled to vote at the 2013 annual meeting, the Registrant will furnish that person without charge a copy of any exhibits listed above. Requests should be addressed to Repligen Corporation, 41 Seyon Street, Waltham, MA 02453.

49

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

	REPLIGEN CORPORATION
Date: March 15, 2013	By:	/S/    WALTER C. HERLIHY
		Walter C. Herlihy President and Chief Executive Officer

POWER OF ATTORNEY

KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears below hereby makes, constitutes and appoints Walter C. Herlihy and Jonathan I. Lieber with full power to act without the other, his true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him and in his name, place and stead, in any and all capacities to sign any or all amendments to this Form 10-K, and to file the same with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorney-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he might or could do in person, hereby ratifying and confirming all that said attorney-in-fact and agents of any of them, or any substitute or substitutes, lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

Signature	Title	Date
/s/    WALTER HERLIHY         Walter C. Herlihy, Ph.D.	President, Chief Executive Officer and Director (Principal executive officer)	March 15, 2013
/s/    JONATHAN I. LIEBER         Jonathan I. Lieber	Chief Financial Officer (Principal financial officer)	March 15, 2013
/S/    WILLIAM J. KELLY         William J. Kelly	Chief Accounting Officer (Principal accounting officer)	March 15, 2013
/S/    KAREN DAWES         Karen Dawes	Chairperson of the Board	March 15, 2013
/S/    GLENN L. COOPER         Glenn L. Cooper, M.D.	Director	March 15, 2013
/S/    ALFRED L. GOLDBERG       Alfred L. Goldberg, Ph.D.	Director	March 15, 2013
/S/    MICHAEL A. GRIFFITH       Michael A. Griffith	Director	March 15, 2013
/S/    EARL W. HENRY       Earl W. Henry, M.D.	Director	March 15, 2013
/S/    THOMAS F. RYAN, JR.         Thomas F. Ryan, Jr.	Director	March 15, 2013

50

EXHIBIT INDEX

Exhibit Number	Document Description
3.1	Restated Certificate of Incorporation dated June 30, 1992 and amended September 17, 1999 (filed as Exhibit 3.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 1999 and incorporated herein by reference) (SEC File No. 000-14656).
3.2	Amended and Restated Bylaws (filed as Exhibit 3.2 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2003 and incorporated herein by reference) (SEC File No. 000-14656).
3.3	Amendment No. 1 to the Amended and Restated Bylaws (filed as Exhibit 3.1 to Repligen Corporation’s Current Report on Form 8-K filed on December 20, 2011 and incorporated herein by reference).
3.4	Amendment No. 2 to the Amended and Restated Bylaws (filed as Exhibit 3.1 to Repligen Corporation’s Current Report on Form 8-K filed on May 25, 2012 and incorporated herein by reference).
4.1	Specimen Stock Certificate (filed as Exhibit 4.1 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.1*	Consulting Agreement, dated November 1, 1981, between Dr. Alexander Rich and Repligen Corporation. (filed as Exhibit 10.2 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.2*	Employment Agreement, dated March 14, 1996, between Repligen Corporation and Walter C. Herlihy (filed as Exhibit 10.3 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.3*	Employment Agreement, dated March 14, 1996, between Repligen Corporation and James R. Rusche (filed as Exhibit 10.4 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.4*	Employment Agreement, dated March 14, 1996, between Repligen Corporation and Daniel P. Witt (filed as Exhibit 10.5 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2002 and incorporated herein by reference) (SEC File No. 000-14656).
10.5*	Employment Offer Letter dated February 29, 2008 by and between Repligen Corporation and William Kelly (filed as Exhibit 10.20 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2008 and incorporated herein by reference).
10.6*	Repligen Executive Incentive Compensation Plan (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on form 8-K filed on December 14, 2005 and incorporated herein by reference).
10.7*	The Amended 1992 Repligen Corporation Stock Option Plan, as amended (filed as Exhibit 4.2 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2000 and incorporated herein by reference) (SEC File No. 000-14656).
10.8*	The Second Amended and Restated 2001 Repligen Corporation Stock Plan (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on September 18, 2008 and incorporated herein by reference).
10.8.1*	The Amended and Restated 2001 Repligen Corporation Stock Option Plan, Form of Incentive Stock Option Agreement (filed as Exhibit 10.14 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2005 and incorporated herein by reference).
10.8.2*	The Amended and Restated 2001 Repligen Corporation Stock Plan, Form of Restricted Stock Agreement (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on January 9, 2006 and incorporated herein by reference).

51

Exhibit Number	Document Description
10.9	Common Stock Purchase Warrant dated April 6, 2007 (filed as Exhibit 4.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2007 and incorporated herein by reference).
10.10#	Manufacturing Transfer Agreement dated as of December 17, 1998 among the Company and Amersham Pharmacia Biotech AB (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended December 31, 1998 and incorporated herein by reference) (SEC File No. 000-14656).
10.11#	License Agreement dated as of July 24, 2000 with University of Michigan (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2000 and incorporated herein by reference) (SEC File No. 000-14656).
10.12	Lease Between Repligen Corporation as Tenant and West Seyon LLC as Landlord, 35 Seyon Street, Waltham, MA (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended December 31, 2001 and incorporated herein by reference) (SEC File No. 000-14656).
10.13#	License Agreement by and between The Scripps Research Institute and Repligen Corporation dated April 6, 2007 (filed as Exhibit 10.18 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2007 and incorporated herein by reference).
10.14#	Settlement and Release Agreement dated April 7, 2008 by and among Repligen Corporation, The Regents of the University of Michigan and Bristol-Myers Squibb Company (filed as Exhibit 10.1 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2008 and incorporated herein by reference).
10.15#	Strategic Supplier Alliance Agreement dated January 28, 2010 by and between Repligen Corporation and GE Healthcare Bio-Sciences AB (filed as Exhibit 10.17 to Repligen Corporation’s Annual Report on Form 10-K for the year ended March 31, 2010 and incorporated herein by reference).
10.16	First Amendment to Lease, dated July 5, 2011, by and between Repligen Corporation and TC Saracen, LLC (filed as Exhibit 10.1 to Repligen’s Current Report on Form 8-K filed on July 5, 2011 and incorporated herein by reference).
10.17	Asset Transfer Agreement by and among Repligen Corporation, Repligen Sweden AB, Novozymes Biopharma DK A/S and Novozymes Biopharma Sweden AB, dated October 27, 2011 (filed as Exhibit 2.1 to Repligen Corporation’s Current Report on Form 8-K filed on October 28, 2011 and incorporated herein by reference).
10.18	Lease Between Repligen Sweden AB (as successor-in-interest to Novozymes Biopharma Sweden AB) as Tenant and i-parken i Lund AB as Landlord, St. Lars Vag 47, 220 09 Lund, Sweden (filed as Exhibit 10.18 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).
10.19#	Amendment No. 1 to Strategic Supplier Alliance Agreement, by and between GE Healthcare Bio-Sciences AB and Repligen Corporation, dated as of October 27, 2011 (filed as Exhibit 10.19 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).
10.20#	Strategic Supplier Alliance Agreement – Contract Manufacturing, by and between GE Healthcare Bio-Sciences AB and Repligen Sweden AB (as successor-in-interest to Novozymes Biopharma Sweden AB), dated as of July 7, 2011 (filed as Exhibit 10.20 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).

52

Exhibit Number	Document Description
10.21#	Amendment to Strategic Supply Alliance Agreement, by and between GE Healthcare Bio-Sciences AB and Repligen Sweden AB (as successor-in-interest to Novozymes Biopharma Sweden AB), dated as of October 27, 2011 (filed as Exhibit 10.21 to Repligen Corporation’s Transition Report on Form 10-K for the year ended December 31, 2011 and incorporated herein by reference).
10.22*	Repligen Corporation 2012 Stock Option and Incentive Plan (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on May 25, 2012 and incorporated herein by reference).
10.23*	Repligen Corporation Non-Employee Directors’ Deferred Compensation Plan (filed as Exhibit 10.2 to Repligen Corporation’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2012 and incorporated herein by reference).
10.24*	Letter Agreement, dated as of September 20, 2012, by and between Repligen Corporation and Jonathan I. Lieber (filed as Exhibit 10.1 to Repligen Corporation’s Current Report on Form 8-K filed on September 21, 2012 and incorporated herein by reference).
10.25#+	License Agreement, dated as of December 28, 2012, by and between Pfizer Inc. and Repligen Corporation.
21.1+	Subsidiaries of the Registrant.
23.1+	Consent of Ernst & Young LLP.
24.1+	Power of Attorney (included on signature page).
31.1+	Rule 13a-14(a)/15d-14(a) Certification.
31.2+	Rule 13a-14(a)/15d-14(a) Certification.
32.1+	Certification Pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101^	The following materials from Repligen Corporation on Form 10-K for the fiscal year ended December 31, 2012, formatted in Extensive Business Reporting Language (XBRL): (i) Consolidated Statements of Operations, (ii) Consolidated Balance Sheets, (iii) Consolidated Statement of Stockholders’ Equity, (iv) Consolidated Statements of Cash Flows, and (v) Notes to Consolidated Financial Statements, tagged as blocks of text.

# Confidential treatment obtained as to certain portions.

* Management contract or compensatory plan or arrangement.

+ Filed herewith.

^ As provided in Rule 406T of Regulation S-T, the XBRL-related information in Exhibit 101 to this Form 10-K is furnished and not filed for purposes of Sections 11 and 12 of the Securities Act of 1933 and Section 18 of the Securities Exchange Act of 1934.

53

INDEX TO FINANCIAL STATEMENTS

	Page
Report of Independent Registered Public Accounting Firm		55
Consolidated Balance Sheets as of December 31, 2012 and December 31, 2011		56
Consolidated Statements of Operations and Comprehensive Income (Loss) for the Year Ended December  31, 2012, the Nine Months Ended December 31, 2011 and 2010 (unaudited) and for the Year Ended March 31, 2011		57
Consolidated Statements of Stockholders’ Equity for the Year Ended December  31, 2012, the Nine Months Ended December 31, 2011 and for the Year Ended March 31, 2011		58
Consolidated Statements of Cash Flows for the Year Ended December  31, 2012, the Nine Months Ended December 31, 2011 and 2010 (unaudited) and for the Year Ended March 31, 2011		59
Notes to Consolidated Financial Statements		60

54

REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

To the Board of Directors and Stockholders of Repligen Corporation:

We have audited the accompanying consolidated balance sheets of Repligen Corporation as of December 31, 2012 and December 31, 2011, and the related consolidated statements of operations and comprehensive income (loss), stockholders’ equity, and cash flows for the year ended December 31, 2012, the nine months ended December, 31, 2011 and the year ended March 31, 2011. These financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on these financial statements based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement. An audit includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements. An audit also includes assessing the accounting principles used and significant estimates made by management, as well as evaluating the overall financial statement presentation. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the financial statements referred to above present fairly, in all material respects, the consolidated financial position of Repligen Corporation at December 31, 2012 and December 31, 2011, and the consolidated results of its operations and its cash flows for the year ended December 31, 2012, the nine months ended December, 31, 2011 and the year ended March 31, 2011, in conformity with U.S. generally accepted accounting principles.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States), Repligen Corporation’s internal control over financial reporting as of December 31, 2012, based on criteria established in Internal Control-Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission and our report dated March 15, 2013 expressed an unqualified opinion thereon.

/s/ Ernst & Young LLP

Boston, Massachusetts

March 15, 2013

55

REPLIGEN CORPORATION

CONSOLIDATED BALANCE SHEETS

	December 31, 2012			December 31, 2011
Assets
Current assets:
Cash and cash equivalents	$	29,209,821		$	11,167,745
Marketable securities		10,845,195			15,421,436
Accounts receivable, less reserve for doubtful accounts of $10,000		4,158,758			2,825,414
Royalties and other receivables		9,130,515			3,206,840
Inventories, net		11,143,695			13,363,073
Deferred tax asset, net		416,580			31,839
Prepaid expenses and other current assets		1,304,887			878,459
Total current assets		66,209,451			46,894,806
Property, plant and equipment, at cost:
Leasehold improvements		5,200,271			5,083,852
Equipment		12,802,978			12,011,154
Furniture and fixtures		1,937,238			1,244,451
Construction in progress		338,814			275,258
Total property, plant and equipment, at cost		20,279,301			18,614,715
Less: Accumulated depreciation		(10,326,840	)		(7,877,296	)
Property, plant and equipment, net		9,952,461			10,737,419
Long-term deferred tax asset, net		2,557,384			—
Long-term marketable securities		9,914,855			9,435,350
Intangible assets, net		7,182,012			7,795,239
Goodwill		994,000			994,000
Restricted cash		200,000			200,000
Total assets	$	97,010,163		$	76,056,814
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable	$	2,454,238		$	1,422,483
Accrued liabilities		8,297,990			6,041,038
Total current liabilities		10,752,228			7,463,521
Deferred tax liability		—			136,881
Other long-term liabilities		2,133,339			2,469,412
Commitments and contingencies (Note 5)
Stockholders’ equity:
Preferred stock, $.01 par value, 5,000,000 shares authorized, no shares issued or outstanding		—			—
Common stock, $.01 par value, 40,000,000 shares authorized, 31,195,041 shares at December 31, 2012 and 30,714,757 shares at December 31, 2011 issued and outstanding		311,950			307,148
Additional paid-in capital		187,051,253			184,872,839
Accumulated other comprehensive income		1,911,970			113,627
Accumulated deficit		(105,150,577	)		(119,306,614	)
Total stockholders’ equity		84,124,596			65,987,000
Total liabilities and stockholders’ equity	$	97,010,163		$	76,056,814

The accompanying notes are an integral part of these consolidated financial statements.

56

REPLIGEN CORPORATION

CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS)

	Year ended December 31,			Nine Months ended December 31,						Year ended March 31,
	2012			2011			2010 (unaudited)			2011
Revenue:
Product revenue	$	41,834,188		$	13,215,053		$	11,810,869		$	14,961,397
Royalty and other revenue		20,432,348			10,235,194			9,573,770			12,329,627
Total revenue		62,266,536			23,450,247			21,384,639			27,291,024
Operating expenses:
Cost of product revenue		24,957,243			5,157,135			4,186,670			5,579,759
Cost of royalty and other revenue		2,213,004			1,315,315			1,160,775			1,537,666
Research and development		10,489,811			9,461,960			8,744,548			12,528,819
Selling, general and administrative		13,226,732			9,050,382			5,580,215			8,018,851
Contingent consideration – fair value adjustments		610,877			—			—			—
Gain on bargain purchase		(314,244	)		(427,478	)		—			—
Total operating expenses		51,183,423			24,557,314			19,672,208			27,665,095
Income (loss) from operations		11,083,113			(1,107,067	)		1,712,431			(374,071	)
Investment income		218,604			161,053			287,430			356,729
Interest expense		(56,714	)		(27,773	)		(12,683	)		(26,167	)
Other income (expense)		26,403			(623,094	)		—			—
Income (loss) before income taxes		11,271,406			(1,596,881	)		1,987,178			(43,509	)
Income tax (benefit) provision		(2,884,631	)		15,744			—			—
Net income (loss)	$	14,156,037		$	(1,612,625	)	$	1,987,178		$	(43,509	)
Earnings (loss) per share:
Basic	$	0.46		$	(0.05	)	$	0.06		$	(0.00	)
Diluted	$	0.45		$	(0.05	)	$	0.06		$	(0.00	)
Weighted average shares outstanding:
Basic		30,914,424			30,774,467			30,778,430			30,781,881
Diluted		31,253,434			30,774,467			30,949,264			30,781,881
Other comprehensive income (loss):
Unrealized gain on investments		7,792			6,338			—			—
Foreign currency translation gain		1,790,551			107,289			—			—
Comprehensive income (loss)	$	15,954,380		$	(1,498,998	)	$	1,987,178		$	(43,509	)

The accompanying notes are an integral part of these consolidated financial statements.

57

REPLIGEN CORPORATION

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY

	Common Stock						Additional Paid-in Capital			Accumulated Other Comprehensive Income		Accumulated Deficit			Stockholders’ Equity
	Number of Shares			Amount
Balance, March 31, 2010		30,761,807		$	307,618		$	183,733,863		$	—	$	(117,921,105	)	$	66,120,376
Net loss													(43,509	)		(43,509	)
Share-based compensation expense								1,003,266								1,003,266
Exercise of stock options		50,450			505			6,066								6,571
Balance, March 31, 2011		30,812,257		$	308,123		$	184,743,195		$	—	$	(117,964,614	)	$	67,086,704
Net loss													(1,612,625	)		(1,612,625	)
Unrealized gain on investments											6,338					6,338
Foreign currency translation adjustment											107,289					107,289
Share-based compensation expense								730,136								730,136
Repurchase and retirement of treasury stock		(100,000	)		(1,000	)		(600,492	)				270,625			(330,867	)
Exercise of stock options		2,500			25											25
Balance, December 31, 2011		30,714,757		$	307,148		$	184,872,839		$	113,627	$	(119,306,614	)	$	65,987,000
Net income													14,156,037			14,156,037
Unrealized gain on investments											7,792					7,792
Foreign currency translation adjustment											1,790,551					1,790,551
Share-based compensation expense								1,024,152								1,024,152
Exercise of stock options		480,284			4,802			1,154,262								1,159,064
Balance, December 31, 2012		31,195,041		$	311,950		$	187,051,253		$	1,911,970	$	(105,150,577	)	$	84,124,596

The accompanying notes are an integral part of these consolidated financial statements.

58

REPLIGEN CORPORATION

CONSOLIDATED STATEMENTS OF CASH FLOWS

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010 (unaudited)			2011
Cash flows from operating activities:
Net income (loss):	$	14,156,037		$	(1,612,625	)	$	1,987,178		$	(43,509	)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization		3,508,592			1,274,597			1,274,247			1,674,528
Stock-based compensation expense		1,024,152			730,136			748,235			1,003,266
Deferred tax expense		(3,143,268	)		15,744			—			—
Gain on bargain purchase		(314,244	)		(427,478	)		—			—
Loss on revaluation of contingent consideration		604,133			28,182			—			—
Loss on disposal of assets		—			2,826			—			5,597
Changes in assets and liabilities:
Accounts receivable		(1,211,343	)		3,551,969			(601,141	)		(689,569	)
Royalties and other receivables		(5,923,675	)		(694,238	)		(450,600	)		(216,602	)
Inventories		2,734,239			(870,252	)		263,570			247,164
Prepaid expenses and other current assets		30,266			(190,007	)		(708,311	)		986,340
Accounts payable		1,001,546			247,222			(291,824	)		(60,404	)
Accrued liabilities		2,083,964			243,182			(408,224	)		383,237
Long-term liabilities		(1,110,791	)		11,487			(25,447	)		(58,285	)
Net cash provided by operating activities		13,439,608			2,310,745			1,787,683			3,231,763
Cash flows from investing activities:
Purchases of marketable securities		(39,109,959	)		(49,465,924	)		(58,095,140	)		(84,329,731	)
Sales of marketable securities		—			26,290,378			—			—
Redemptions of marketable securities		43,214,487			45,624,819			54,225,000			83,650,417
Acquisition of assets of BioFlash Partners, LLC		—			—			(300,000	)		(300,000	)
Acquisition of assets and liabilities of Novozymes		—			(26,884,428	)		—			—
Purchases of property, plant and equipment		(1,263,647	)		(575,455	)		(317,982	)		(524,666	)
Net cash provided by (used in) investing activities		2,840,881			(5,010,610	)		(4,488,122	)		(1,503,980	)
Cash flows from financing activities:
Exercise of stock options		1,159,064			25			25,758			6,571
Repurchase and retirement of treasury stock		—			(330,867	)		—			—
Principal payments under capital lease obligations		—			—			(56,850	)		(56,850	)
Net cash provided by (used in) financing activities		1,159,064			(330,842	)		(31,092	)		(50,279	)
Effect of exchange rate changes on cash and cash equivalents		602,523			(5,092	)		—			—
Net increase (decrease) in cash and cash equivalents		18,042,076			(3,035,799	)		(2,731,531	)		1,677,504
Cash and cash equivalents, beginning of period		11,167,745			14,203,544			12,526,040			12,526,040
Cash and cash equivalents, end of period	$	29,209,821		$	11,167,745		$	9,794,509		$	14,203,544
Supplemental disclosure of non-cash investing activities:
Income taxes paid	$	140,000		$	—		$	—		$	—
Contingent consideration transferred in the Novozymes Acquisition	$	—		$	1,610,560		$	—		$	—

The accompanying notes are an integral part of these consolidated financial statements.

59

REPLIGEN CORPORATION

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

(Information for the nine months ended December 31, 2010 is unaudited)

1. Organization and Nature of Business

Repligen Corporation (“Repligen” or the “Company”) is a life sciences company that develops, manufactures and markets high-value, consumable bioprocessing products for life sciences companies and biopharmaceutical manufacturing companies worldwide. The Company is a world-leading manufacturer of both native and recombinant forms of Protein A, critical reagents used in biomanufacturing to separate and purify monoclonal antibodies, a type of biologic drug. Repligen also supplies several growth factor products used to increase cell culture productivity during the biomanufacturing process. In the burgeoning area of disposable biomanufacturing technologies, the Company has developed and currently markets a series of OPUS (Open-Platform, User-Specified) chromatography columns for use in clinical-scale manufacturing. The Company generally manufactures and sells Protein A and growth factors to life sciences companies under long-term supply agreements and sells its chromatography columns, as well as media and quality test kits, directly to biopharmaceutical companies or contract manufacturing organizations. Repligen refers to these activities as its bioprocessing business. The Company manufactures its products in production facilities in the United States and Sweden.

Historically, Repligen also conducted activities aimed at developing proprietary therapeutic drug candidates, often with a potential of entering into a collaboration with a larger commercial stage pharmaceutical or biotechnology company in respect of these programs. In addition, the Company has out-licensed certain intellectual property to Bristol-Myers Squibb Company, or Bristol, from which Repligen receives royalties on Bristol’s net sales in the United States of their product Orencia^®. As part of Repligen’s strategic decision in 2012 to focus the Company’s efforts on its core bioprocessing business, the Company scaled back efforts on its clinical development programs and increased its efforts to find collaboration partners to finish their development and, if successful, commercialize these therapeutic drug candidates.

The Company is subject to a number of risks typically associated with companies in the biotechnology industry. These risks principally include the Company’s dependence on key customers, development by the Company or its competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with the FDA and other governmental regulations and approval requirements, as well as the ability to grow the Company’s business and obtain adequate funding to finance this growth.

2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States (“GAAP”) requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Consolidation

The consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Repligen Europe Limited and Repligen Sweden AB. All significant intercompany accounts and transactions have been eliminated in consolidation.

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Foreign Currency

The Company translates the assets and liabilities of foreign subsidiaries at rates in effect at the end of the reporting period. Revenues and expenses are translated at average rates in effect during the reporting period. Translation adjustments are included in accumulated other comprehensive income.

Revenue Recognition

Product Sales

The Company generates product revenues from the sale of bioprocessing products to customers in the pharmaceutical and process chromatography industries. The Company recognizes revenue related to product sales upon delivery of the product to the customer as long as there is persuasive evidence of an arrangement, the sales price is fixed or determinable and collection of the related receivable is reasonably assured. Determination of whether these criteria have been met is based on management’s judgments primarily regarding the fixed nature of the fee charged for the product delivered and the collectability of those fees. The Company has a few longstanding customers who comprise the majority of revenue and have excellent payment histories and therefore the Company does not require collateral. The Company has had no significant write-offs of uncollectible invoices in the periods presented.

At the time of sale, the Company also evaluates the need to accrue for warranty and sales returns. The supply agreements the Company has with its customers and related purchase orders identify the terms and conditions of each sale and the price of the goods ordered. Due to the nature of the sales arrangements, inventory produced for sale is tested for quality specifications prior to shipment. Since the product is manufactured to order and in compliance with required specifications prior to shipment, the likelihood of sales return, warranty or other issues is largely diminished. Sales returns and warranty issues are infrequent and have had nominal impact on the Company’s consolidated financial statements historically.

Orencia Royalty

In April 2008, the Company settled its outstanding litigation with Bristol and began recognizing royalty revenue in fiscal year 2009 for Bristol’s net sales in the United States of Orencia^®, which is used in the treatment of rheumatoid arthritis. Pursuant to the settlement with Bristol (see Note 9), the Company recognized royalty revenue of $14,753,000 for the fiscal year ended December 31, 2012, $8,769,000 for the nine-month fiscal year ended December 31, 2011 and $10,251,000 for the fiscal year ended March 31, 2011. Revenue earned from Bristol royalties is recorded in the periods when it is earned based on royalty reports sent by Bristol to the Company. The Company has no continuing obligations to Bristol as a result of this settlement. The Company’s royalty agreement with Bristol provides that the Company will receive such royalty payments from Bristol through December 31, 2013.

Therapeutics Licensing Agreements

Activities under licensing agreements are evaluated in accordance with ASC 605-25 to determine if they represent a multiple element revenue arrangement. The Company identifies the deliverables included within the agreement and evaluates which deliverables represent separate units of accounting. The Company accounts for those components as separate units of accounting if the following two criteria are met:

• The delivered item or items have value to the customer on a stand-alone basis.

• If there is a general right of return relative to the delivered items, delivery or performance of the undelivered items is considered probable and within our control.

Factors considered in this determination include, among other things, whether any other vendors sell the items separately and if the licensee could use the delivered item for its intended purpose without the receipt of

61

the remaining deliverables. If multiple deliverables included in an arrangement are separable into different units of accounting, the Company allocates the arrangement consideration to those units of accounting. The amount of allocable arrangement consideration is limited to amounts that are fixed or determinable. Arrangement consideration is allocated at the inception of the arrangement to the identified units of accounting based on their relative selling price. Revenue is recognized for each unit of accounting when the appropriate revenue recognition criteria are met.

Future milestone payments, if any, under a license agreement will be recognized under the provisions of ASC 605-28, which the Company adopted on January 1, 2011. The Company has elected to recognize a payment that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is substantive if:

• It can only be achieved based in whole or in part on either (1) the Company’s performance or (2) on the occurrence of a specific outcome resulting from the Company’s performance;

• There is substantive uncertainty at the date an arrangement is entered into that the event will be achieved; and

• It would result in additional payments being due to the entity.

The Company believes that the clinical milestone payments pursuant to the license agreement with Pfizer, Inc. (“Pfizer”), as described in Note 10, are substantive and thus will be recognized when achieved. The commercial milestone payments and royalty payments received under license agreements, if any, will be recognized as revenue when they are earned.

Research and Development Agreements

In the fiscal year ended December 31, 2012, the Company recognized $803,000 of revenue from sponsored research and development projects under agreements with the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, GoFar, and the Friedreich’s Ataxia Research Alliance.

For the nine-month fiscal year ended December 31, 2011, the Company recognized $1,466,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, Go Friedreich’s Ataxia Research (“GoFar”), and the Friedreich’s Ataxia Research Alliance. For the nine-month period ended December 31, 2010, the Company recognized $1,102,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. For the nine months ended December 31, 2010, the Company also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

In the fiscal year ended March 31, 2011, the Company recognized $1,346,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. During the year ended March 31, 2011, the Company also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

Research revenue is recognized when the expense has been incurred and services have been performed. Determination of which costs incurred qualify for reimbursement under the terms of the Company’s contractual agreements and the timing of when such costs were incurred involves the judgment of management. The

62

Company’s calculations are based upon the agreed-upon terms as stated in the arrangements. However, should the estimated calculations change or be challenged by other parties to the agreements, research revenue may be adjusted in subsequent periods. The calculations have not historically changed or been challenged and the Company does not anticipate any subsequent change in its revenue related to sponsored research and development projects.

There have been no material changes to the Company’s initial estimates related to revenue recognition in any periods presented in the accompanying consolidated financial statements.

Risks and Uncertainties

The Company evaluates its operations periodically to determine if any risks and uncertainties exist that could impact its operations in the near term. The Company does not believe that there are any significant risks which have not already been disclosed in the consolidated financial statements. A loss of certain suppliers could temporarily disrupt operations, although alternate sources of supply exist for these items. The Company has mitigated these risks by working closely with key suppliers, identifying alternate sources and developing contingency plans.

Cash, Cash Equivalents and Marketable Securities

At December 31, 2012 and December 31, 2011, the Company’s investments included money market funds as well as short-term and long-term marketable securities. Marketable securities are investments with original maturities of greater than 90 days. Long-term marketable securities are securities with maturities of greater than one year. The average remaining contractual maturity of marketable securities at December 31, 2012 is approximately 9.9 months.

Investments in debt securities consisted of the following at December 31, 2012:

	December 31, 2012
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	2,000,897	$	353	$	(7	)	$	2,001,243
Corporate and other debt securities		8,835,098		8,854		—			8,843,952
		10,835,995		9,207		(7	)		10,845,195
Long-term marketable securities:
U.S. Government and agency securities		5,198,264		2,747		—			5,201,011
Corporate and other debt securities		4,711,679		3,525		(1,360	)		4,713,844
		9,909,943		6,272		(1,360	)		9,914,855
Total	$	20,745,938	$	15,479	$	(1,367	)	$	20,760,050

At December 31, 2012, the Company’s investments included seven debt securities in unrealized loss positions with a total unrealized loss of approximately $1,000 and a total fair market value of approximately $2,667,000. All investments with gross unrealized losses have been in unrealized loss positions for less than 12 months. The unrealized losses were caused primarily by current economic and market conditions. There was no change in the credit risk of the securities. The Company does not intend to sell any investments in an unrealized loss position and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases. There were no realized gains or losses on the investments for the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011 or the fiscal year ended March 31, 2011.

63

Investments in debt securities consisted of the following at December 31, 2011:

	December 31, 2011
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	8,373,355	$	3,126	$	(233	)	$	8,376,248
Corporate and other debt securities		7,046,222		3,336		(4,370	)		7,045,188
		15,419,577		6,462		(4,603	)		15,421,436
Long-term marketable securities:
U.S. Government and agency securities		8,399,428		2,223		(91	)		8,401,560
Corporate and other debt securities		1,031,443		2,347		—			1,033,790
		9,430,871		4,570		(91	)		9,435,350
Total	$	24,850,448	$	11,032	$	(4,694	)	$	24,856,786

The contractual maturities of debt securities at December 31, 2012 were as follows:

	Amortized Cost		Fair Value
Due in 1 year or less	$	10,835,995	$	10,845,195
Due in 1 to 2 years		9,909,943		9,914,855
	$	20,745,938	$	20,760,050

Fair Value Measurement

In determining the fair value of its assets and liabilities, the Company uses various valuation approaches. The Company employs a hierarchy for inputs used in measuring fair value that maximizes the use of observable inputs and minimizes the use of unobservable inputs by requiring that observable inputs be used when available. Observable inputs are inputs that market participants would use in pricing the asset or liability based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the asset or liability and are developed based on the best information available in the circumstances. The fair value hierarchy is broken down into three levels based on the source of inputs as follows:

Level 1	—	Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access.
Level 2	—	Valuations based on quoted prices for similar assets or liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active and models for which all significant inputs are observable, either directly or indirectly.
Level 3	—	Valuations based on inputs that are unobservable and significant to the overall fair value measurement.

The availability of observable inputs can vary among the various types of financial assets and liabilities. To the extent that the valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. In certain cases, the inputs used to measure fair value may fall into different levels of the fair value hierarchy. In such cases, for financial statement disclosure purposes, the level in the fair value hierarchy within which the fair value measurement is categorized is based on the lowest level input that is significant to the overall fair value measurement.

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The Company’s fixed income investments are comprised of obligations of U.S. government agencies, corporate debt securities and other interest bearing securities. These investments have been initially valued at the transaction price and subsequently valued, at the end of each reporting period, utilizing third party pricing services or other market observable data. The pricing services utilize industry standard valuation models, including both income and market based approaches and observable market inputs to determine value. These observable market inputs include reportable trades, benchmark yields, credit spreads, broker/dealer quotes, bids, offers, current spot rates and other industry and economic events. The Company validates the prices provided by third party pricing services by reviewing their pricing methods and matrices, obtaining market values from other pricing sources, analyzing pricing data in certain instances and confirming that the relevant markets are active. After completing its validation procedures, the Company did not adjust or override any fair value measurements provided by the pricing services as of December 31, 2012.

The following fair value hierarchy table presents information about each major category of the Company’s assets measured at fair value on a recurring basis as of December 31, 2012:

	Fair value measurement at reporting date using:
	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Total
Assets:
Money market funds	$	7,891,062	$	—	$	—	$	7,891,062
U.S. Government and agency securities		2,901,209		5,201,011		—		8,102,220
Corporate and other debt securities		—		13,557,796		—		13,557,796
Total	$	10,792,271	$	18,758,807	$	—	$	29,551,078

The Company has no other assets or liabilities for which fair value measurement is either required or has been elected to be applied, other than the liabilities for contingent consideration recorded in connection with the Novozymes Acquisition and the acquisition of the assets of BioFlash Partners, LLC (“BioFlash”). The contingent consideration related to Novozymes is valued using management’s estimates of expected future milestone payments based upon a probability weighted analysis of amounts to be paid to Novozymes Denmark. The contingent consideration related to BioFlash is valued using management’s estimates of royalties to be paid to the former shareholders of BioFlash based on sales of the acquired assets. These valuations are Level 3 valuations as the primary inputs are unobservable. Changes in the fair value of contingent consideration in the year ended December 31, 2012 are primarily attributable to changes in the probability of the Company making certain contingent payments. The following table provides a roll forward of the fair value of the contingent consideration:

Balance at December 31, 2011	$	2,197,226
Additions		—
Payments		(35,000	)
Changes in fair value		736,850
Balance at December 31, 2012	$	2,899,076

There were no remeasurements to fair value during the year ended December 31, 2012 of financial assets and liabilities that are not measured at fair value on a recurring basis.

Inventories

Inventories relate to the Company’s bioprocessing business. The Company values inventory at cost or, if lower, fair market value, using the first-in, first-out method. The Company reviews its inventories at least

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quarterly and records a provision for excess and obsolete inventory based on its estimates of expected sales volume, production capacity and expiration dates of raw materials, work-in process and finished products. Expected sales volumes are determined based on supply forecasts provided by key customers for the next three to 12 months. The Company writes down inventory that has become obsolete, inventory that has a cost basis in excess of its expected net realizable value, and inventory in excess of expected requirements to cost of product revenue. Manufacturing of bioprocessing finished goods is done to order and tested for quality specifications prior to shipment. Reserves for excess and obsolete inventory were $154,000 and $149,000 as of December 31, 2012 and 2011, respectively. At both December 31, 2010 and March 31, 2011, reserves for excess and obsolete inventory were $50,000.

A change in the estimated timing or amount of demand for the Company’s products could result in additional provisions for excess inventory quantities on hand. Any significant unanticipated changes in demand or unexpected quality failures could have a significant impact on the value of inventory and reported operating results. During all periods presented in the accompanying financial statements, there have been no material adjustments related to a revised estimate of inventory valuations.

Work-in-process and finished products inventories consist of material, labor, outside processing costs and manufacturing overhead. Inventories consist of the following:

	December 31, 2012		December 31, 2011
Raw Materials	$	4,064,317	$	3,563,395
Work-in-process		4,112,478		5,936,578
Finished products		2,966,900		3,863,100
Total	$	11,143,695	$	13,363,073

Accrued Liabilities

The Company estimates accrued liabilities by identifying services performed on the Company’s behalf, estimating the level of service performed and determining the associated cost incurred for such service as of each balance sheet date. Examples of estimated accrued expenses include: (1) Fees paid to contract manufacturers in conjunction with the production of clinical materials. These expenses are normally determined through a contract or purchase order issued by the Company; (2) Service fees paid to organizations for their performance in conducting clinical trials. These expenses are determined by contracts in place for those services and communications with project managers on costs which have been incurred as of each reporting date; and (3) Professional and consulting fees incurred with law firms, audit and accounting service providers and other third party consultants. These expenses are determined by either requesting those service providers to estimate unbilled services at each reporting date for services incurred or tracking costs incurred by service providers under fixed fee arrangements.

The Company has processes in place to estimate the appropriate amounts to record for accrued liabilities, which principally involve the applicable personnel reviewing the services provided. In the event that the Company does not identify certain costs that have begun to be incurred or the Company under or over-estimates the level of services performed or the costs of such services, the reported expenses for that period may be too low or too high. The date on which certain services commence, the level of services performed on or before a given date, and the cost of such services often require the exercise of judgment. The Company makes these judgments based upon the facts and circumstances known at the date of the financial statements.

Income Taxes

Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Valuation allowances are provided, if, based upon the weight of available evidence, it is more likely than not that some or all of the deferred tax assets will not be realized. The Company accounts for uncertain tax positions

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using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors including, but not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. The Company evaluates this tax position on a quarterly basis. The Company also accrues for potential interest and penalties, related to unrecognized tax benefits in income tax expense.

Depreciation

Depreciation is calculated using the straight-line method over the estimated useful life of the asset as follows:

Classification	Estimated Useful Life
Leasehold improvements	Shorter of the term of the lease or estimated useful life
Equipment	Three to eight years
Furniture and fixtures	Three years

For depreciation of property and equipment, the Company expensed approximately $2,492,000 in the year ended December 31, 2012, $1,117,000 and $1,141,000 in the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, as well as $1,496,000 in the fiscal year ended March 31, 2011. These amounts include depreciation of assets recorded under capitalized lease agreements of approximately $82,000 in the nine months ended December 31, 2010 and $82,000 in the fiscal year ended March31, 2011. Assets recorded under capital leases were fully depreciated at December 31, 2011.

Earnings (Loss) Per Share

Basic earnings (loss) per share is computed by dividing net income (loss) available to common shareholders by the weighted average number of common shares outstanding during the period. Diluted earnings per share is computed by dividing net income available to common shareholders by the weighted-average number of common shares and dilutive common share equivalents then outstanding. Potential common share equivalents consist of restricted stock awards and the incremental common shares issuable upon the exercise of stock options and warrants. Under the treasury stock method, unexercised “in-the-money” stock options are assumed to be exercised at the beginning of the period or at issuance, if later. The assumed proceeds are then used to purchase common shares at the average market price during the period. Share-based payment awards that entitle their holders to receive non-forfeitable dividends before vesting are considered participating securities and are included in the calculation of basic and diluted earnings per share.

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A reconciliation of basic and diluted share amounts is as follows:

	Year ended December 31,		Nine Months ended December 31,					Year ended March 31,
	2012		2011			2010		2011
Numerator:
Net income (loss)	$	14,156,037	$	(1,612,625	)	$	1,987,178	$	(43,509	)
Denominator:
Basic weighted average common shares outstanding		30,914,424		30,774,467			30,778,430		30,781,881
Weighted average common stock equivalents from assumed exercise of stock options and restricted stock awards		339,010		—			170,834		—
Diluted weighted average common shares outstanding		31,253,434		30,774,467			30,949,264		30,781,881
Basic net income (loss) per common share	$	0.46	$	(0.05	)	$	0.06	$	(0.00	)
Diluted net income (loss) per common share	$	0.45	$	(0.05	)	$	0.06	$	(0.00	)

At December 31, 2012, there were outstanding options to purchase 2,315,090 shares of the Company’s common stock at a weighted average exercise price of $4.20 per share. For the fiscal year ended December 31, 2012, 1,296,700 shares of the Company’s common stock were excluded from the calculation of diluted earnings per share because the exercise prices of the stock options were greater than or equal to the average price of the common shares, and were therefore anti-dilutive.

At December 31, 2011, there were outstanding options to purchase 2,823,400 shares of the Company’s common stock at a weighted average exercise price of $4.05 per share.

At December 31, 2010, there were outstanding options to purchase 2,566,450 shares of the Company’s common stock at a weighted average exercise price of $4.08 per share. For the nine-month fiscal year ended December 31, 2010, 1,771,100 shares of the Company’s common stock were excluded from the calculation of diluted earnings per share because the exercise prices of the stock options were greater than or equal to the average price of the common shares, and were therefore anti-dilutive.

Diluted weighted average shares outstanding for the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011 do not include the impact of 2,823,400 and 2,580,600 outstanding potential common shares for stock options, respectively, as they would be anti-dilutive. Accordingly, basic and diluted net loss per share are the same for the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011.

Segment Reporting

The Company views its operations, makes decisions regarding how to allocate resources and manages its business as one operating segment. As a result, the financial information disclosed herein represents all of the material financial information related to the Company’s principal operating segment.

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The following table represents the Company’s total revenue by geographic area (based on the location of the customer):

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
United States		46	%		48	%		48	%		50	%
Sweden		42	%		44	%		45	%		42	%
Other		12	%		8	%		7	%		8	%
Total		100	%		100	%		100	%		100	%

The following table represents the Company’s total assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	58,356,697	$	44,223,080
Sweden		38,653,466		31,833,734
Total	$	97,010,163	$	76,056,814

The following table represents the Company’s long-lived assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	16,537,804	$	13,380,836
Sweden		14,262,908		15,781,172
Total	$	30,800,712	$	29,162,008

Concentrations of Credit Risk and Significant Customers

Financial instruments that subject the Company to significant concentrations of credit risk primarily consist of cash and cash equivalents, marketable securities and accounts receivable. Per the Company’s investment policy, cash equivalents and marketable securities are invested in financial instruments with high credit ratings and credit exposure to any one issue, issuer (with the exception of U.S. treasury obligations) and type of instrument is limited. At December 31, 2012 and 2011, the Company had no investments associated with foreign exchange contracts, options contracts or other foreign hedging arrangements.

Concentration of credit risk with respect to accounts receivable is limited to customers to whom the Company makes significant sales. While a reserve for the potential write-off of accounts receivable is maintained, the Company has not written off any significant accounts to date. To control credit risk, the Company performs regular credit evaluations of its customers’ financial condition.

Revenue from significant customers as a percentage of the Company’s total revenue is as follows:

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
Orencia® Royalties from Bristol		24	%		37	%		37	%		38	%
Bioprocessing Customer A		42	%		44	%		45	%		42	%

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Significant accounts receivable balances as a percentage of the Company’s total trade accounts receivable and royalties and other receivable balances are as follows:

	December 31, 2012			December 31, 2011
Orencia® Royalties from Bristol		31	%		53	%
Bioprocessing Customer A		21	%		31	%
Pfizer		38	%		—

Goodwill, Other Intangible Assets and Acquisitions

Acquisitions

Total consideration transferred for acquisitions (see Note 11) is allocated to the assets acquired and liabilities assumed, if any, based on their fair values at the dates of acquisition. The fair value of identifiable intangible assets is based on detailed valuations that use information and assumptions determined by management. Any excess of purchase price over the fair value of the net tangible and intangible assets acquired is allocated to goodwill. Any excess of the fair value of the net tangible and intangible assets acquired over the purchase price is recognized in the statement of operations. The fair value of contingent consideration includes estimates and judgments made by management regarding the probability that future contingent payments will be made and the extent of royalties to be earned in excess of the defined minimum royalties. Management updates these estimates and the related fair value of contingent consideration at each reporting period. Changes in the fair value of contingent consideration are recorded in the consolidated statements of operations.

The Company uses the income approach to determine the fair value of certain identifiable intangible assets including customer relationships and developed technology. This approach determines fair value by estimating after-tax cash flows attributable to these assets over their respective useful lives and then discounting these after-tax cash flows back to a present value. The Company bases its assumptions on estimates of future cash flows, expected growth rates, expected trends in technology, etc. Discount rates used to arrive at a present value as of the date of acquisition are based on the time value of money and certain industry-specific risk factors.

Goodwill

Goodwill is not amortized and is reviewed for impairment at least annually. There was no evidence of impairment to goodwill at December 31, 2012. There were no goodwill impairment charges during the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 or the fiscal year ended March 31, 2011.

Intangible Assets

Intangible assets are amortized over their useful lives using the estimated economic benefit method, as applicable, and the amortization expense is recorded within cost of product revenue and selling, general and administrative expense in the statements of operations. Intangible assets and their related useful lives are reviewed at least annually to determine if any adverse conditions exist that would indicate the carrying value of these assets may not be recoverable. More frequent impairment assessments are conducted if certain conditions exist, including a change in the competitive landscape, any internal decisions to pursue new or different technology strategies, a loss of a significant customer, or a significant change in the marketplace, including changes in the prices paid for our products or changes in the size of the market for our products. An impairment results if the carrying value of the asset exceeds the estimated fair value of the asset based on the sum of the future undiscounted cash flows expected to result from the use and disposition of the asset. If the estimate of an intangible asset’s remaining useful life is changed, the remaining carrying amount of the intangible asset is amortized prospectively over the revised remaining useful life. The Company continues to believe that its intangible assets are recoverable at December 31, 2012.

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Intangible assets consisted of the following at December 31, 2012:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,452,729	$	(360,748	)		8
Patents		240,000		(87,500	)		8
Customer relationships		6,872,383		(934,852	)		8
Total intangible assets	$	8,565,112	$	(1,383,100	)		8

Intangible assets consisted of the following at December 31, 2011:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,413,564	$	(184,402	)		8
Patents		240,000		(57,500	)		8
Customer relationships		6,508,147		(124,570	)		8
Total intangible assets	$	8,161,711	$	(366,472	)		8

Amortization expense for amortized intangible assets was approximately $1,017,000 for the year ended December 31, 2012, $158,000 for the nine-month fiscal year ended December 31, 2011, $134,000 for the nine-month period ended December 31, 2010 and $179,000 for the fiscal year ended March 31, 2011. The Company expects to record amortization expense of approximately $1,000,000 in each of the next five years.

Stock Based Compensation

The Company measures stock-based compensation cost at the grant date based on the estimated fair value of the award, and recognizes it as expense over the employee’s requisite service period on a straight-line basis. The Company records the expense for share-based awards subject to performance-based milestone vesting over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates whether the achievement of a performance-based milestone is probable as of the reporting date. The Company has no awards that are subject to market conditions. The Company recognizes stock-based compensation expense based upon options that are ultimately expected to vest, and accordingly, such compensation expense has been adjusted by an amount of estimated forfeitures.

The Company uses the Black-Scholes option pricing model to calculate the fair value of share-based awards on the grant date. The following assumptions are used in calculating the fair value of share-based awards:

Expected term—The expected term of options granted represents the period of time for which the options are expected to be outstanding. The expected term is presumed to be the midpoint between the vesting date and the end of the contractual term. In addition, for purposes of estimating the expected term, the Company has aggregated all individual option awards into one group as the Company does not expect substantial differences in exercise behavior among its employees.

Expected volatility—The expected volatility is a measure of the amount by which the Company’s stock price is expected to fluctuate during the expected term of options granted. The Company determines the expected volatility based primarily upon the historical volatility of the Company’s common stock over a period commensurate with the option’s expected term, exclusive of any events not reasonably anticipated to recur over the option’s expected term.

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Risk-free interest rate—The risk-free interest rate is the implied yield available on U.S. Treasury zero-coupon issues with a remaining term equal to the option’s expected term on the grant date.

Expected dividend yield—The Company has never declared or paid any cash dividends on any of its capital stock and does not expect to do so in the foreseeable future. Accordingly, the Company uses an expected dividend yield of zero to calculate the grant-date fair value of a stock option.

Estimated forfeiture rates—The Company has applied, based on an analysis of its historical forfeitures, annual forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees to all unvested stock options as of December 31, 2012. The Company reevaluates this analysis periodically and adjusts these estimated forfeiture rates as necessary. Ultimately, the Company will only recognize expense for those shares that vest.

3. Income Taxes

Income tax data for the year ended December 31, 2012, the nine months ended December 31, 2011 and the year ended March 31, 2011:

	December 31, 2012			December 31, 2011			March 31, 2011
The components of income from operations before income taxes are as follows:
Domestic	$	11,175,638		$	(1,845,024	)	$	(43,509	)
Foreign		95,768			248,143			—
Total	$	11,271,406		$	(1,596,881	)	$	(43,509	)
The current and deferred components of the provision for income taxes on operations are as follows:
Current	$	312,630		$	—		$	—
Deferred		(3,197,261	)		15,774			—
Total	$	(2,884,631	)	$	15,774		$	—
The jurisdictional components of the provision for income taxes on operations are as follows:
Federal	$	(2,915,673	)	$	48,000		$	—
State		115,307			—			—
Foreign		(84,265	)		(32,226	)		—
Total	$	(2,884,631	)	$	15,774		$	—

At December 31, 2012, the Company had net operating loss carryforwards of approximately $44,678,000 and business tax credits carryforwards of approximately $2,160,000 available to reduce future federal income taxes, if any. The U.S. federal net operating loss includes $441,000 related to excess tax deductions from share-based payments, the tax benefit of which will be recognized as an increase to additional paid in capital when the deduction reduces current taxes payable. The net operating loss and business tax credits carryforwards will continue to expire at various dates through December 2032. The net operating loss and business tax credit carryforwards are subject to review and possible adjustment by the Internal Revenue Service and may be limited in the event of certain changes in the ownership interest of significant stockholders.

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The Company’s consolidated deferred tax assets (liabilities) consist of the following:

	December 31, 2012			December 31, 2011
Deferred tax assets:
Temporary timing differences	$	4,152,000		$	4,277,000
Net operating loss carryforwards		15,041,000			20,065,000
Tax business credits carryforwards		2,160,000			4,166,000
Total deferred tax assets		21,353,000			28,508,000
Valuation allowance		(18,307,000	)		(28,476,000	)
Net deferred tax assets	$	3,046,000		$	32,000
Deferred tax liabilities:
Goodwill	$	(72,000	)	$	(48,000	)
Acquired intangibles		—			(89,000	)
Net deferred tax assets (liabilities)	$	2,974,000		$	(105,000	)

The net change in the total valuation allowance was a decrease of $10,169,000 in the year ended December 31, 2012. The valuation allowance increased by $73,000 for the nine months ended December 31, 2011 and increased by $2,227,000 for the year ended March 31, 2011. As of September 30, 2012, the Company’s U.S. net operating losses (“NOL’s”) and other deferred tax assets were fully offset by a valuation allowance primarily because the Company was in a cumulative loss position and did not have sufficient history of income to conclude that it was more likely than not that the Company would be able to realize the tax benefits of those deferred tax assets. In the fourth quarter of 2012, the Company entered into a three-year cumulative pre-tax income position and concluded that it was more likely than not that it will generate sufficient taxable income in 2013 based on its 2013 projections to realize the tax benefit of a portion of its deferred tax assets. Thus, the Company reversed $3,021,000 of the deferred tax asset valuation allowance in the U.S in the fourth quarter of 2012. The amount is recorded as a benefit for income taxes in the Company’s consolidated statements of operations and comprehensive income (loss). The Company concluded that realization of deferred tax assets beyond December 31, 2013 is not more likely than not as a result of the fact that the Company will not receive royalty payments from Bristol on U.S. net sales of Orencia after December 31, 2013, and as such, the Company continues to maintain a valuation allowance against those deferred tax assets estimated to reverse beyond 2013.

The reconciliation of the federal statutory rate to the effective income tax rate for the year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011 is as follows:

	Period Ended,
	December 31, 2012					December 31, 2011					March 31, 2011
Income (loss) before income taxes	$	11,271,406			%	$	(1,596,881	)		%	$	(43,509	)		%
Expected tax (recovery) at statutory rate		3,944,996		35.0	%		(542,939	)	(34.0	)%		(14,793	)	(34.0	)%
Adjustments due to:
Difference between U.S. and foreign tax		(8,332	)	(0.1	)%		(19,287	)	(1.2	)%		—		(0.0	)%
State income and franchise taxes		357,866		3.2	%		52,905		3.3	%		96,141		221.0	%
Business tax credits		(67,276	)	(0.6	)%		(68,926	)	(4.3	)%		(66,126	)	(152.0	)%
Transaction costs		—		0.0	%		240,842		15.1	%		—		0.0	%
Gain on bargain purchase		(82,422	)	(0.7	)%		(112,427	)	(7.0	)%		—		(0.0	)%
Permanent differences		242,629		2.1	%		218,989		13.7	%		250,483		575.7	%
Change in valuation allowance		(7,272,092	)	(64.5	)%		246,587		15.4	%		(265,706	)	(610.7	)%
Provision (benefit) for income taxes	$	(2,884,631	)	(25.6	)%	$	15,744		1.0	%	$	—		(0.0	)%

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At December 31, 2012 and 2011 as well as March 31, 2011, the Company had no material unrecognized tax benefits.

The Company recognizes interest and penalties related to uncertain tax positions in income tax expense. No interest and penalties have been recognized by the Company to date.

The fiscal years ended March 31, 2007 through March 31, 2011 as well as the nine-month fiscal year ended December 31, 2011 and the year ended December 31, 2012 are subject to examination by the federal and state taxing authorities. Currently, a corporate excise tax audit is underway in the Commonwealth of Massachusetts for the fiscal years ended March 31, 2007 and 2008. To date, no assessments have been made and the Company continues to believe no reserve is required.

At December 31, 2012, the Company has not provided for U.S. income taxes or foreign withholding taxes on outside basis differences of foreign subsidiaries of approximately $477,000 as it is the Company’s current intention to permanently reinvest these earnings outside the U.S.

4. Stockholders’ Equity

Common Stock and Warrants

At December 31, 2012, the Company has reserved 3,893,210 shares of common stock pursuant to the Plans, as described below. On April 6, 2007, the Company issued warrants to an individual at Scripps to purchase up to 150,000 shares of common stock at $0.01 per share, as discussed in Note 11. The warrants have a seven-year term and are exercisable based on performance criteria as detailed in the warrant agreement. At this time, the Company does not believe that the performance criteria are probable of being achieved in the near future.

Stock-Based Compensation

The Company recorded stock-based compensation expense of approximately $1,024,000 for the year ended December 31, 2012 for share-based awards granted under the Second Amended and Restated 2001 Repligen Corporation Stock Plan (the “2001 Plan”) and the Repligen Corporation 2012 Stock Option and Incentive Plan (the “2012 Plan,” and collectively with the 2001 Plan and the 1992 Repligen Corporation Stock Option Plan, the “Plans”). We recorded stock-based compensation expense of approximately $730,000 for the nine-month fiscal year ended December 31, 2011, and $748,000 for the nine-month period ended December 31, 2010 for share-based awards granted under the Plans. For the fiscal year ended March 31, 2011, we recorded stock-based compensation expense of approximately $1,003,000 for stock options granted under the 2001 Plan.

The following table presents stock-based compensation expense in the Company’s consolidated statements of operations:

	Year ended December 31, 2012		Nine Months ended December 31,				Year ended March 31, 2011
			2011		2010 (unaudited)
Cost of product revenue	$	45,000	$	35,000	$	38,000	$	48,000
Research and development		219,000		191,000		164,000		226,000
Selling, general and administrative		760,000		504,000		546,000		729,000
Total	$	1,024,000	$	730,000	$	748,000	$	1,003,000

The 2012 Plan allows for the granting of incentive and nonqualified options to purchase shares of common stock, restricted stock and other equity awards. Incentive options granted to employees under the Plans generally vest over a four to five-year period, with 20%-25% vesting on the first anniversary of the date of grant and the remainder vesting in equal yearly installments thereafter. Nonqualified options issued to non-employee directors and consultants under the Plans generally vest over one year. Options granted under the Plans have a maximum term of ten years from the date of grant and generally, the exercise price of the stock options equals the fair

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market value of the Company’s common stock on the date of grant. At December 31, 2012, options to purchase 2,315,090 shares were outstanding under the Plans. At December 31, 2012, 1,578,120 shares were available for future grant under the 2012 Plan.

The Company uses the Black-Scholes option pricing model to calculate the fair value of share-based awards on the grant date. The fair value of share-based awards granted during the year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 and the fiscal year ended March 31, 2011 were calculated using the following estimated assumptions:

	Year ended December 31,	Nine Months ended December 31,		Years ended March 31,
	2012	2011	2010	2011
Expected term (years)	6.5	6.5	6.5	6.5
Volatility	49.76% - 53.54%	53.09% - 55.76%	57.58% - 63.60%	55.94% - 63.60%
Risk-free interest rate	0.89% - 1.06%	1.25% - 2.38%	1.81% - 2.62%	1.81% - 2.83%
Expected dividend yield	—	—	—	—

Information regarding option activity for the year ended December 31, 2012 under the Plans is summarized below:

	Options Outstanding			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term (in years)		Aggregate Intrinsic Value
Options outstanding at December 31, 2011		2,823,400		$	4.05
Granted		368,690			3.65
Exercised		(609,400	)		3.06
Forfeited/cancelled		(267,600	)		4.44
Options outstanding at December 31, 2012		2,315,090		$	4.20		6.16	$	4,854,412
Options exercisable at December 31, 2012		1,447,600		$	4.39		4.96	$	2,783,183
Vested and expected to vest at December 31, 2012 (1)		2,186,609		$	4.21		6.05	$	4,570,615

(1) This represents the number of vested options as of December 31, 2012 plus the number of unvested options expected to vest as of December 31, 2012 based on the unvested outstanding options at December 31, 2012 adjusted for estimated forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees.

The aggregate intrinsic value in the table above represents the total pre-tax intrinsic value (the difference between the closing price of the common stock on December 31, 2012 of $6.28 per share and the exercise price of each in-the-money option) that would have been received by the option holders had all option holders exercised their options on December 31, 2012. The aggregate intrinsic value of stock options exercised during the year ended December 31, 2012 was approximately $1,384,000. The aggregate intrinsic value of stock options exercised during the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010 was approximately $8,000 and $43,000, respectively. The aggregate intrinsic value of stock options exercised during the fiscal year ended March 31, 2011 was approximately $76,000.

The weighted average grant date fair value of options granted during the year ended December 31, 2012 was $3.62. The weighted average grant date fair value of options granted during the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010 was $1.89 and $1.95, respectively. The weighted average grant date fair value of options granted during the fiscal year ended March 31, 2011 was $2.11. The total fair value of stock options that vested during the year ended December 31, 2012 was approximately $931,000. The total fair value of stock options that vested during the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010 was approximately $804,000 and

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$817,000, respectively. The total fair value of stock options that vested during the fiscal year ended March 31, 2011 was approximately $993,000.

As of December 31, 2012, there was $1,605,995 of total unrecognized compensation cost related to unvested share-based awards. This cost is expected to be recognized over a weighted average remaining requisite service period of 2.76 years. We expect 739,009 unvested options to vest over the next five years.

5. Commitments and Contingencies

Lease Commitments

In 2001, the Company entered into a ten-year lease agreement for approximately 25,000 square feet of space located in Waltham, Massachusetts to be used for its corporate headquarters, manufacturing, research and development, and marketing and administrative operations. In July 2011, the Company amended this agreement to expand the lease to cover approximately 56,000 square feet and to extend the term of the lease by eleven years, which expires on May 31, 2023. In connection with this lease agreement, the Company issued a letter of credit in the amount of $200,000 to the lessor. The letter of credit is collateralized by a certificate of deposit held by the bank that issued the letter of credit. The certificate of deposit is classified as restricted cash in the accompanying consolidated balance sheets.

In 2007, the Company entered into a five-year lease agreement for approximately 2,500 square feet of space in Waltham, Massachusetts to provide for expanded manufacturing operations. Adjacent to this space, the Company entered into a two-year lease in 2008 for approximately 7,350 square feet of additional space to be used for expanded manufacturing and administrative operations. Both of these leases expired on December 31, 2012 and we are now on a month-to-month basis.

Following the completion of the Novozymes Acquisition, the Company now leases four adjacent buildings in Lund, Sweden totaling approximately 45,000 square feet of space used primarily for biologics manufacturing and administrative operations. The lease for three buildings totaling approximately 41,000 square feet expires on June 30, 2017 while the lease for the fourth building with approximately 4,000 square feet of space expires on September 30, 2019.

Obligations under non-cancelable operating leases, including the facility leases discussed above, as of December 31, 2012 are approximately as follows:

Years Ending	Operating Leases
December 31, 2013	$	2,222,000
December 31, 2014		2,222,000
December 31, 2015		2,222,000
December 31, 2016		2,222,000
December 31, 2017		1,655,000
Thereafter		5,611,000
Minimum lease payments	$	16,154,000

Rent expense charged to operations under operating leases was approximately $2,183,000 for the fiscal year ended December 31, 2012, $528,000 and $510,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, and $686,000 for the fiscal year ended March 31, 2011. As of December 31, 2012 and December 31, 2011, the Company had deferred rent liabilities of $329,000 and $15,000, respectively, related to the escalating rent provisions for the Waltham headquarters.

Licensing and Research Agreements

The Company licenses certain technologies that are, or may be, incorporated into its technology under several agreements and also has entered into several clinical research agreements which require the Company to

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fund certain research projects. Generally, the license agreements require the Company to pay annual maintenance fees and royalties on product sales once a product has been established using the technologies. The Company recorded research and development expenses associated with license agreements of approximately $55,000 for the fiscal year ended December 31, 2012, $525,000 and $343,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, as well as $374,000 for the fiscal year ended March 31, 2011.

In October 2009, the Company entered into an exclusive worldwide commercial license agreement with Families of Spinal Muscular Atrophy (see Note 10). The initial license fee of $500,000 and a related sublicense fee of $175,000 were charged to research and development expenses in the fiscal year ended March 31, 2010. A related sublicense fee of $65,000 was charged to research and development expenses in the fiscal year ended March 31, 2011. A related milestone payment of $500,000 was charged to research and development expenses in the nine month fiscal year ended December 31, 2011. If all milestones are achieved, total financial obligations under this agreement, including milestone payments, sublicense fees, and other charges, could total approximately $16,000,000. Given the uncertain nature of such a development program, the likelihood that products or services will result from the research program is not known at this time.

Purchase Orders, Supply Agreements and Other Contractual Obligations

In the normal course of business, the Company has entered into purchase orders and other agreement with manufacturers, distributors and others. Outstanding obligations at December 31, 2012 of approximately $2,872,000 are expected to be completed within one year.

6. Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consist of the following:

	December 31, 2012		December 31, 2011
Equipment maintenance and services		747,273		424,328
Prepaid insurance		365,167		251,418
Interest receivable		140,363		106,695
Clinical and research expenses		15,354		13,714
Other		36,730		82,304
Total	$	1,304,887	$	878,459

7. Accrued Liabilities

Accrued liabilities consist of the following:

	December 31, 2012		December 31, 2011
Employee compensation	$	3,634,839	$	2,741,738
Royalty and license fees		1,459,680		499,776
Contingent consideration		1,376,877		35,000
Unearned revenue		599,120		469,046
Professional fees		418,800		871,086
VAT liabilities		98,162		566,542
Research and development		18,300		142,695
Other accrued expenses		692,212		715,155
Total	$	8,297,990	$	6,041,038

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8. Employee Benefit Plans

In the U.S., the Repligen Corporation 401(k) Savings and Retirement Plan (the “401(k) Plan”) is a qualified defined contribution plan in accordance with Section 401(k) of the Internal Revenue Code. All U.S. employees over the age of 21 are eligible to make pre-tax contributions up to a specified percentage of their compensation. Under the 401(k) Plan, the Company may, but is not obligated to match a portion of the employees’ contributions up to a defined maximum. The match is calculated on a calendar year basis. The Company matched approximately $103,000 for the year ended December 31, 2012, $102,000 for the nine-month fiscal year ended December 31, 2011, and $108,000 for both the nine-month period ended December 31, 2010 and the year ended March 31, 2011.

In Sweden, the Company contributes to a government-mandated occupational pension plan that is a qualified defined contribution plan. All employees in Sweden are eligible for this pension plan. The Company pays premiums to a third party occupational pension specialist who administers the pension plan. These premiums are based on various factors including each employee’s age, salary, employment history and selected benefits in the pension plan. When an employee terminates or retires, these premium payments cease for that employee and the Company has no further pension-related obligations for that employee. For the fiscal year ended December 31, 2012, the Company contributed approximately $532,000 to the pension plan. For the period from the completion of the Novozymes Acquisition on December 20, 2011 to December 31, 2011, the Company contributed approximately $10,000 to the pension plan.

9. Royalty Arrangement with Bristol Myers Squibb Company (“Bristol”)

In 2008, the Company together with the University of Michigan entered into a settlement agreement with Bristol related to alleged patent infringement of a certain patent related to the treatment of rheumatoid arthritis. The settlement provides for Bristol to pay royalties on the United States net sales of Orencia^® for any clinical indication at a rate of 1.8% for the first $500 million of annual net sales, 2.0% for the next $500 million of annual net sales and 4% of annual net sales in excess of $1 billion for each year from January 1, 2008 until December 31, 2013.

Pursuant to the Bristol Settlement, the Company recognized royalty revenue of $14,753,000 for the year ended December 31, 2012, $8,769,000 and $7,739,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, and $10,251,000 for the fiscal year ended March 31, 2011.

The Company must also remit to the University of Michigan 15% of all royalty revenue received from Bristol. Royalty expense was $2,213,000 for the year ended December 31, 2012, $1,315,000 and $1,161,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, and $1,537,000 for the fiscal year ended March 31, 2011. Royalty expense is included on the statements of operations under the line item “Cost of royalty and other revenue.”

10. License Agreements

Pfizer

On December 28, 2012, the Company entered into an exclusive worldwide outlicensing agreement (the “License Agreement”) with Pfizer to advance the SMA program, which is led by RG3039 and also includes backup compounds and enabling technologies. Under the terms of the License Agreement, the Company received a $5 million upfront payment on January 22, 2013 and is entitled to receive up to $65 million in potential future milestone payments, a portion of which may be owed to third parties. These potential payments are approximately equally divided between milestones related to clinical development and initial commercial sales in specific geographies. In addition, the Company is entitled to receive royalties on any future sales of RG3039 or

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any SMA compounds developed under the License Agreement. The License Agreement also provides for tiered and increasing royalty rates which begin in the high single-digits for RG-3039 or lesser amounts for any backup compounds developed under the License Agreement. The Company’s receipt of these royalties is subject to an obligation under an existing in-license agreement and other customary offsets and deductions. Royalties are payable, on a country-by-country basis, for a duration based upon the later of (a) expiration of the licensed patent(s) or (b) a predetermined time after the first commercial sale of the first such product in such country.

Pursuant to the License Agreement, Pfizer will assume virtually all of the costs associated with completing the required clinical trials for the SMA program as well as obtaining FDA approval of the respective NDA. The Company is obligated to conduct additional activities in support of this program, which include completion of the second cohort of the ongoing Phase I trial and supporting the transition of the program to Pfizer. The Company will also provide specific technology transfer services to Pfizer who will then assume full responsibility for the SMA program moving forward, including the conduct of any registration trials necessary for any product approvals. The Company expects to complete its obligation with respect to this program in the first half of 2013. Pfizer may terminate the license agreement at any time for convenience. There are no refund provisions in the License Agreement.

Activities under this agreement were evaluated in accordance with ASC 605-25 to determine if they represented a multiple element revenue arrangement. The Company identified the following deliverables in the Pfizer agreement:

• An exclusive license to research, develop, manufacture, commercialize and use RG3039 and backup compounds for the treatment of SMA and other disorders (the “License”);

• Research and development services designed to transition the SMA program to Pfizer pursuant to a transition plan (the “Transition Services”) ;

• The completion of the second cohort of a phase I clinical trial that was underway at the time the License Agreement was signed; and

• An inventory of RG3039, that could be used in clinical development, specifically to complete the phase I clinical trial, referenced immediately above (the “Clinical Trial Material”).

The deliverables outlined above were deemed to have stand-alone value and to meet the criteria to be accounted for as separate units of accounting. Factors considered in this determination included, among other things, whether any other vendors sell the items separately or whether or not Pfizer had the ability to resell and if Pfizer could use the delivered item for its intended purpose without the receipt of the remaining deliverables. The amount of allocable arrangement consideration is limited to amounts that are fixed or determinable. Arrangement consideration is allocated at the inception of the arrangement to the identified units of accounting based on their relative selling price.

The Company identified the arrangement consideration to allocate among the units of accounting as the $5.0 million non-refundable up-front payment and excluded the potential milestone payments provided for in the License Agreement from the arrangement consideration as they were not considered fixed or determinable at the time the License Agreement was signed. Because Repligen had not sold these items on a standalone basis previously, there was no vendor-specific objective evidence of selling price. Furthermore, the Company did not have detailed third-party evidence of selling price, and as a result used a best estimate of selling price for each item. In determining these prices, the Company considered what it would be willing to sell the items for on a standalone basis, what the market would bear for such items and what another party might charge for these items.

The Company used a discounted cash flow analysis to determine the value of the license. Key assumptions in the analysis included: the estimated market size for a compound targeted at SMA, the estimated remaining costs of development and time to commercialization, and the probability of successfully developing and commercializing the program. A change in the key assumptions used to determine best estimate of selling price for each of the deliverables would not have a significant effect on the allocation of arrangement consideration.

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Based on this analysis, the Company allocated $4,876,000 to the value of the license and recognized this amount as revenue in the year ended December 31, 2012 upon delivery as the risks and rewards associated with the License transferred at that time.

The remaining $124,000 of value was allocated based on the following:

• The estimated selling price of the Transition Services was approximately $600,000 resulting in consideration allocation of approximately $76,000. Repligen was able to derive a price for these services, in part because they are similar to services provided by a contract research organization. The selling price of the Transition Services was based on the Company’s internal FTE costs and external costs that it expects to incur to transition the program to Pfizer. The Company applied a mark-up on the internal FTE costs consistent with that of contract research organizations.

• The estimated selling price of the completion of the second cohort of the clinical trial was approximately $275,000 resulting in consideration allocation of approximately $35,000. This estimated selling price is based on the estimated, remaining costs to complete this cohort. Since the costs are pursuant to an arrangement negotiated with a third-party (the clinical site), the Company believes that the external cost estimate included in the agreement represents the best estimate of selling price for this unit of accounting.

• The estimated selling price of the Clinical Trial Material was approximately $105,000 resulting in consideration allocation of approximately $13,000. The estimated selling price is based upon the cost of procuring such material from the contract manufacturing organization that made the material. Since these costs were incurred pursuant to an arrangement negotiated with a third-party (the contract manufacturing organization), the Company believes that the costs included in the agreement represents the best estimate of selling price for this unit of accounting.

The Company intends to recognize the revenues related to the transfer of Clinical Trial Material upon transfer of title and risk of loss to Pfizer. The Company expects to recognize revenues related to the Transition Services and the completion of the second cohort ratably over the first six months of 2013.

In addition to the $5 million up-front payment, the Company is also eligible to receive $65 million in potential milestone payments comprised of: (i) up to $30 million related to the achievement of specified clinical milestone events; and (ii) up to $35 million related to the achievement of specified commercial sales events, specifically first commercial sale in specific territories. The Company may receive all, or a portion of, the first clinical milestone of $2 million in 2013 depending upon the development path chosen by Pfizer. If the Company receives a portion of this milestone, it expects to receive the balance of it by the end 2014.

Any future royalty payments, under the License Agreement will be recognized as revenue when they are earned.

The Scripps Research Institute

On April 6, 2007, the Company entered into an exclusive worldwide commercial license agreement (“Scripps License Agreement”) with The Scripps Research Institute (“Scripps”). Pursuant to the License Agreement, the Company obtained a license to use, commercialize and sublicense certain patented technology and improvements thereon, owned or licensed by Scripps, relating to compounds that may have utility in treating Friedreich’s ataxia, an inherited neurodegenerative disease. Research in tissues derived from patients, as well as from mice, indicates that the licensed compounds increase production of the protein frataxin, which suggests potential utility of these compounds in slowing or stopping progression of the disease. There are currently no approved treatments for Friedreich’s ataxia in the U.S.

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Pursuant to the Scripps License Agreement, the Company agreed to pay Scripps an initial license fee of $300,000, certain royalty and sublicense fees and, in the event that the Company achieves specified developmental and commercial milestones, certain additional milestone payments. Total future milestone payments, if all milestones were achieved, would be approximately $4,300,000. In addition, the Company issued Scripps and certain of its designees 87,464 shares of the Company’s common stock, which had a value of $300,000 on the date of issuance.

In connection with the Scripps License Agreement, the Company issued warrants to an individual at Scripps to purchase up to 150,000 shares of common stock. The warrants have a seven-year term and are exercisable based on performance criteria as detailed in the warrant agreement governing such warrants. No expense has been recorded related to these warrants through December 31, 2012, as none of the performance criteria have been achieved. At this time, the Company does not believe that the performance criteria are probable of being achieved.

The Scripps License Agreement with Scripps expires or may be terminated (i) when all of the royalty obligations under the License Agreement expire; (ii) at any time by mutual written consent; (iii) by Scripps if the Company (a) fails to make payments under the License Agreement, (b) fails to achieve certain developmental and commercial objectives, (c) becomes insolvent, (d) is convicted of a felony relating to the manufacture, use or sale of the licensed technology, or (e) defaults in its performance under the License Agreement; or (iv) by the Company upon 90 days written notice.

Families of Spinal Muscular Atrophy

On October 22, 2009, the Company entered into an exclusive worldwide commercial license agreement (“FSMA License Agreement”) with Families of Spinal Muscular Atrophy (“FSMA”). Pursuant to the FSMA License Agreement, the Company obtained an exclusive license to develop and commercialize certain patented technology, and improvements thereon, owned or licensed by FSMA, relating to compounds that may have utility in treating spinal muscular atrophy (“SMA”). SMA is an inherited neurodegenerative disease in which a defect in the survival motor neuron gene (“SMN”) results in low levels of the protein SMN and leads to progressive damage to motor neurons, loss of muscle function and, in many patients, early death.

Pursuant to the FSMA License Agreement, the Company paid FSMA an initial license fee of $500,000 and a related sublicense fee of $175,000 in the year ended March 31, 2010. In April 2011, the Company paid an additional $500,000 milestone payment to FSMA. These license fees were recorded as research and development expense in the statements of operations. If all milestones are achieved, total financial obligations under this agreement, including milestone payments, sublicense fees, and other charges, could total approximately $16,000,000. Given the uncertain nature of such a development program, the likelihood that products or services will result from the research program is not known at this time. The Company has therefore ascribed no value to the license or the related liability.

The License Agreement with FSMA expires or may be terminated (i) on the later of: (a) when all related patents have expired or been abandoned, or (b) 10 years following the first commercial sale of a licensed product; (ii) by FSMA if the Company (a) fails to make payments under the License Agreement, (b) fails to use commercially reasonable efforts towards development and commercial objectives, (c) fails to maintain the required insurance or becomes insolvent, or (d) defaults in its performance under the License Agreement.

11. Acquisitions

Novozymes Biopharma Sweden AB

On December 20, 2011, the Company acquired the Novozymes Biopharma Business from Novozymes, for total consideration transferred of $28,495,000. The terms of the transaction required that the payment be

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denominated in Euros, but it is reflected here in U.S. dollars for presentation purposes. The Novozymes Acquisition diversified and expanded Repligen’s bioprocessing product offering and customer base while doubling the Company’s manufacturing capacity. The terms of the acquisition included an upfront payment of $26,884,000 and future potential milestone payments totaling up to €4,000,000, if specific sales targets are met for certain products by various dates ending on December 31, 2014 and upon the transfer of manufacturing processes for certain products. This business operates as the Company’s wholly-owned subsidiary, Repligen Sweden AB. The €4,000,000 contingent consideration had an initial probability-weighted fair value at acquisition of $1,611,000.

Consideration Transferred

The Company accounted for the Novozymes Acquisition as the purchase of a business under GAAP. Under the acquisition method of accounting, the assets and certain liabilities of the Novozymes Biopharma Business were recorded as of the acquisition date, at their respective fair values, and consolidated with those of Repligen. The fair value of the net assets acquired was originally estimated to be $28,922,000, which exceeded the total consideration transferred of $28,495,000. Accordingly, the Company recognized the excess of the fair value of the net assets over the purchase price of approximately $427,000 as a gain on bargain purchase. During the year ended December 31, 2012, the fair value of the net assets acquired increased to $29,236,000, due primarily to working capital adjustments on the purchased assets. These adjustments resulted in an additional gain on bargain purchase of $314,000 which was recorded in the year ended December 31, 2012 and is shown separately within income from operations in the consolidated statements of operations.

The Company believes that it was able to acquire the Novozymes Biopharma Business for less than the fair value of its assets because of (i) the Company’s unique position as a market leader in this industry segment and (ii) the seller’s intent to exit this industry segment, which was only a small part of the seller’s overall business and no longer fit its strategy.

The preparation of the valuation to support the fair value of acquired assets and liabilities required the use of significant assumptions and estimates. Critical estimates included, but were not limited to, future expected cash flows, including projected revenues and expenses, and the applicable discount rates. These estimates were based on assumptions that the Company believes to be reasonable. However, actual results may differ from these estimates.

The total consideration transferred follows:

Cash consideration	$	26,445,000
Estimated fair value of contingent consideration		1,611,000
Total consideration transferred	$	28,056,000

The fair value of contingent consideration was determined based upon a probability weighted analysis of expected future milestone payments to be made to the seller. The Company could make payments of up to €4,000,000 if specific sales targets are met for certain products by various dates ending on December 31, 2014 and upon the transfer of manufacturing processes for certain products. The Company recorded a $618,000 increase in the liability for contingent consideration in the year ended December 31, 2012 to reflect updates to the Company’s probability analysis and for the time value of money. At December 31, 2012, $1,322,000 of the liability for contingent consideration is included in current liabilities and $1,033,000 is included in other long-term liabilities in the consolidated balance sheet. The liability will be remeasured at each reporting period until the contingency is resolved.

The Company incurred approximately $1.7 million in transaction costs related to the Novozymes Acquisition. The transaction costs are included in selling, general and administrative expenses in the consolidated statements of operations in the period ended December 31, 2011.

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Fair Value of Net Assets Acquired

The following chart summarizes the allocation of the fair value of assets acquired and liabilities assumed:

Accounts receivable	$	5,088,000
Inventory		10,497,000
Prepaid expenses		180,000
Fixed assets		9,089,000
Customer relationships and acquired technology		6,705,000
Deferred tax liability		(198,000	)
Accounts payable and other liabilities assumed		(2,563,000	)
Net assets acquired	$	28,798,000
Less total consideration transferred		(28,056,000	)
Gain on bargain purchase	$	742,000

The Company finalized its fixed asset valuation analysis in the quarter ended September 30, 2012 and the purchase price allocation is now considered final.

BioFlash Partners, LLC

On January 29, 2010, the Company acquired the assets of BioFlash Partners, LLC (“BioFlash”), including a technology platform for the production of pre-packed, “plug and play” chromatography columns for total consideration transferred of $2.6 million. This patented technology enables economical production of chromatography columns in a format that is ready for use in the production of a broad range of biopharmaceuticals, including monoclonal antibodies, vaccines and recombinant proteins. The terms of the acquisition included an upfront payment of $1.8 million and a milestone payment of $300,000 that was made in November 2010.

The Company manufactures and sells these pre-packed columns under the brand name OPUS. OPUS pre-packed chromatography columns have the potential to improve manufacturing efficiencies by reducing time for column packing, set-up and cleaning.

Total consideration transferred was $2,640,000 comprised of cash payments of $2,080,000 and the fair value of contingent consideration of $560,000.

The fair value of contingent consideration was determined based upon a probability weighted analysis of expected future royalty payments to be made to former shareholders of BioFlash. The liability for contingent consideration is included in current and long-term liabilities on the consolidated balance sheets and will be remeasured at each reporting period until the contingency is resolved.

Allocation of Consideration Transferred

The following chart summarizes the allocation of consideration transferred:

Intangible assets subject to amortization	$	1,430,000
Goodwill		994,000
Equipment		216,000
Total	$	2,640,000

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12. Selected Quarterly Financial Data (Unaudited)

The following table contains consolidated statements of operations information for each of the previous eight quarters. The Company believes that the following information reflects all normal recurring adjustments necessary for a fair presentation of the information for the periods presented. The operating results for any quarter are not necessarily indicative of results for any future period.

	December 31, 2012			September 30, 2012			June 30, 2012			March 31, 2012			December 31, 2011			September 30, 2011		June 30, 2011			March 31, 2011
	(in thousands, except per share amounts)
Revenue:
Product revenue	$	9,710		$	11,123		$	11,659		$	9,342		$	3,114		$	5,742	$	4,359		$	3,150
Royalty and other revenue		9,104			3,981			3,865			3,482			4,051			2,889		3,295			2,756
Total revenue		18,814			15,104			15,524			12,824			7,165			8,631		7,654			5,906
Operating expenses:
Cost of product revenue		5,920			6,419			7,345			5,273			1,511			2,093		1,553			1,393
Cost of royalty and other revenue		620			594			537			462			481			418		416			376
Research and development		2,343			2,433			2,906			2,808			2,870			3,075		3,517			3,785
Selling, general and administrative		3,253			3,126			3,418			3,428			4,268			2,493		2,289			2,438
Contingent consideration – fair value adjustments		267			344			—			—			(427	)		—		—			—
Gain on bargain purchase		—			—			—			(314	)		(427	)		—		—			—
Total operating expenses		12,403			12,916			14,206			11,657			8,703			8,079		7,775			7,992
Income (loss) from operations		6,411			2,188			1,318			1,167			(1,538	)		552		(121	)		(2,086	)
Investment income		62			95			29			31			43			53		66			69
Interest expense		(14	)		7			(27	)		(22	)		(28	)		—		—			(13	)
Other income (expense)		(41	)		(500	)		458			109			(623	)		—		—			—
Income (loss) before income taxes		6,418			1,790			1,778			1,285			(2,146	)		605		(55	)		(2,030	)
Income tax provision (benefit)		(3,135	)		(16	)		208			59			16			—		—			—
Net income (loss)	$	9,553		$	1,806		$	1,570		$	1,226		$	(2,162	)	$	605	$	(55	)	$	(2,030	)
Earnings (loss) per share:
Basic	$	0.31		$	0.06		$	0.05		$	0.04		$	(0.07	)	$	0.02	$	(0.00	)	$	(0.06	)
Diluted	$	0.30		$	0.06		$	0.05		$	0.04		$	(0.07	)	$	0.02	$	(0.00	)	$	(0.06	)
Weighted average shares outstanding:
Basic		31,132			30,948			30,845			30,730			30,715			30,797		30,812			30,782
Diluted		31,600			31,256			31,149			31,010			30,715			30,934		30,812			30,782

84

EX-10.25

Exhibit 10.25

EXECUTION VERSION

LICENSE AGREEMENT

by and between

PFIZER INC.

and

REPLIGEN CORPORATION

DECEMBER 28, 2012

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

EXECUTION VERSION

TABLE OF CONTENTS

1.	DEFINITIONS AND INTERPRETATION	1
	1.1.        Defined Terms	1
	1.2.        Interpretation	1
2.	LICENSE GRANTS	2
	2.1.        Exclusive Licenses from Company to Pfizer	2
	2.2.        Non-Exclusive Licenses from Company to Pfizer	2
	2.3.        Pfizer Sublicensees	2
	2.4.        Direct Licenses to Affiliates	3
	2.5.        No Implied Rights	3
	2.6.        Retained Rights	3
	2.7.        Acknowledgements; Covenants	3
3.	PAYMENTS BY PFIZER TO Company	4
	3.1.        Initial Upfront Payment	4
	3.2.        Clinical and Regulatory Milestones	4
	3.3.        Royalty Payments	6
	3.4.        Reports and Payments	9
	3.5.        Pfizer Right of Setoff	11
	3.6.        No Guarantee of Success	12
4.	TRANSFERS; TRANSITION; PRODUCT DEVELOPMENT, MANUFACTURING AND COMMERCIALIZATION	13
	4.1.        General	13
	4.2.        Transfers	13
	4.3.        Transition	14
	4.4.        Manufacturing	14
	4.5.        Diligence	15
	4.6.        Regulatory Approvals	15
	4.7.        Commercialization Activities	15
	4.8.        Other Pfizer Programs	16

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

5.	INTELLECTUAL PROPERTY	16
	5.1.        Patent Rights	16
	5.2.        Right to Enforce	17
	5.3.        Pfizer Right to Defend	18
	5.4.        Recovery	18
	5.5.        Withdrawal	19
	5.6.        Recording	19
6.	CONFIDENTIALITY	19
	6.1.        Confidentiality	19
	6.2.        Authorized Disclosure	19
	6.3.        SEC Filing and Other Disclosures	20
	6.4.        Residual Knowledge Exception	21
	6.5.        Public Announcements; Publications	21
7.	REPRESENTATIONS AND WARRANTIES	22
	7.1.        Mutual Representations and Warranties	22
	7.2.        Mutual Covenants	22
	7.3.        Representations and Warranties of Company	22
	7.4.        Company Covenants	25
	7.5.        Representation by Legal Counsel	27
	7.6.        Disclaimer	27
8.	TERM AND TERMINATION	27
	8.1.        Term	27
	8.2.        Termination by Company	27
	8.3.        Termination by Pfizer	27
	8.4.        Termination of FSMA-Company Agreement	28
	8.5.        Effects of Termination	28
	8.6.        Provision for Insolvency	30

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

ii

EXECUTION VERSION

9.	LIMITATION ON LIABILITY, INDEMNIFICATION AND INSURANCE	31
	9.1.        No Consequential Damages	31
	9.2.        Indemnification by Pfizer	31
	9.3.        Indemnification by Company	31
	9.4.        Procedure	32
	9.5.        Insurance	33
10.	MISCELLANEOUS	34
	10.1.      Assignment	34
	10.2.      Further Actions	34
	10.3.      Force Majeure	34
	10.4.      Notices	34
	10.5.      Amendment	36
	10.6.      Waiver	36
	10.7.      Severability	36
	10.8.      Descriptive Headings	36
	10.9.      Export Control	36
	10.10.    Dispute Resolution	36
	10.11.    Governing Law	37
	10.12.    Consent to Jurisdiction	37
	10.13.    Entire Agreement	37
	10.14.    Independent Contractors	38
	10.15.    Counterparts	38
	10.16.    No Third Party Rights or Obligations	38

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

iii

EXECUTION VERSION

EXHIBITS

Exhibit A        Defined Terms

Exhibit B        Company Patent Rights Existing as of the Effective Date

Exhibit C        Compounds Existing as of the Effective Date

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

iv

EXECUTION VERSION

SCHEDULES

Schedule 4.3.1	Key Provisions for the Transition Services Agreement
	Appendix A: Clinical Responsibilities
Schedule 4.3.2	Activities in Relation to Existing Clinical Trial
Schedule 6.5.1	Company Press Release
Schedule 7.3.1	Intellectual Property Exceptions re: Ownership
Schedule 7.3.8	Intellectual Property Exceptions re: Know-How
Schedule 7.3.10	Disclosed Third Party Agreements
Schedule A-1	Inventory

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

v

EXECUTION VERSION

LICENSE AGREEMENT

This License Agreement (the “Agreement”) is entered into as of December 28, 2012 (the “Effective Date”), by and between Pfizer Inc., a corporation organized and existing under the laws of Delaware and having a principal place of business at 235 East 42nd Street, New York, NY 10017 (“Pfizer”) and Repligen Corporation, a corporation organized and existing under the laws of Delaware and having its principal place of business at 41 Seyon St, Waltham, MA 02453 (“Company”). Pfizer and Company may each be referred to herein individually as a “Party” and collectively as the “Parties.”

WHEREAS, Company owns or otherwise controls certain patents, patent applications, technology, know-how, scientific and technical information and other proprietary rights and information relating to the identification, research and development of the Compounds (as defined below);

WHEREAS, Pfizer has extensive experience and expertise in the development and commercialization of pharmaceutical products, and desires to acquire an exclusive license in the Territory (as defined below) under Company’s patents, patent applications, technology, know-how, scientific and technical information and other proprietary rights and information relating to the Compounds and Licensed Products;

WHEREAS, subject to the terms of this Agreement, Company wishes to grant to Pfizer, and Pfizer wishes to receive from Company, an exclusive license in the Territory to use, research, develop, manufacture, commercialize, make, use, sell, offer for sale and import Compounds and Licensed Products throughout the Field (as defined below).

NOW THEREFORE, in consideration of the mutual promises and covenants set forth below and other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the Parties hereby agree as follows:

1. DEFINITIONS AND INTERPRETATION.

1.1. Defined Terms. Capitalized terms not otherwise defined herein shall have the meanings set forth in Exhibit A.

1.2. Interpretation. Except where the context expressly requires otherwise, (a) the use of any gender herein shall be deemed to encompass references to either or both genders, and the use of the singular shall be deemed to include the plural (and vice versa), (b) the words “include”, “includes” and “including” shall be deemed to be followed by the phrase “without limitation”, (c) the word “will” shall be construed to have the same meaning and effect as the word “shall”, (d) any definition of or reference to any agreement, instrument or other document herein shall be construed as referring to such agreement, instrument or other document as from time to time amended, supplemented or otherwise modified (subject to any restrictions on such

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

1

EXECUTION VERSION

amendments, supplements or modifications set forth herein), (e) any reference herein to any Person shall be construed to include the Person’s successors and assigns, (f) the words “herein”, “hereof” and “hereunder”, and words of similar import, shall be construed to refer to this Agreement in its entirety and not to any particular provision hereof, (g) all references herein to Sections, Exhibits or Schedules shall be construed to refer to Sections, Exhibits or Schedules of this Agreement, and references to this Agreement include all Exhibits and Schedules hereto, (h) the word “notice” means notice in writing (whether or not specifically stated) and shall include notices, consents, approvals and other written communications contemplated under this Agreement, (i) provisions that require that a Party, the Parties or any committee hereunder “agree,” “consent” or “approve” or the like shall require that such agreement, consent or approval be specific and in writing, whether by written agreement, letter, approved minutes or otherwise (but excluding e-mail and instant messaging), (j) references to any specific law, rule or regulation, or article, section or other division thereof, shall be deemed to include the then-current amendments thereto or any replacement or successor law, rule or regulation thereof, and (k) the term “or” shall be interpreted in the inclusive sense commonly associated with the term “and/or.”

2. LICENSE GRANTS.

2.1. Exclusive Licenses from Company to Pfizer. Effective as of the Effective Date, Company hereby grants to Pfizer exclusive (even as to Company) license under Company’s right, title and interest in the Company Intellectual Property to (a) research, Develop, Manufacture, Commercialize and use, including to make, sell, offer for sale and import, any and all Compounds and Licensed Products throughout the Field and (b) undertake discovery and research compounds directed towards SMA Compounds/Products, including as possible candidates to become Compounds.

2.2. Non-Exclusive Licenses from Company to Pfizer. Effective as of the Effective Date, Company hereby grants to Pfizer and its Affiliates a non-exclusive, royalty-free, perpetual license under the Company Know-How owned by Company to conduct research, Development and Manufacturing in all fields. The foregoing license shall not be sublicenseable.

2.3. Pfizer Sublicensees. With respect to the license granted by Company to Pfizer pursuant to Section 2.1, Pfizer shall have the right to enter into one or more Sublicense Agreements, provided that entry into such Sublicense Agreements shall not relieve Pfizer of any of its obligations hereunder. Each Sublicense Agreement shall be consistent with the terms of this Agreement and shall expressly provide that such Sublicense shall terminate immediately upon the termination or expiration of the term of this Agreement. [***].

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

2

EXECUTION VERSION

2.4. Direct Licenses to Affiliates. Pfizer may, from time to time, request that Company grant licenses directly to Affiliates of Pfizer by giving written notice, upon receipt of which Company agrees to enter into and sign a separate direct license agreement with such designated Affiliate of Pfizer. All such direct license agreements shall be consistent with the terms and conditions of this Agreement, except for such modifications as may be required by applicable Laws in the country in which the direct license will be exercised. The Parties further agree to make any amendments to this Agreement that are necessary to conform the combined terms of such direct licenses and this Agreement to the terms of this Agreement as set forth on the Effective Date. All costs of making such direct license agreement(s), including Company’s reasonable attorneys’ fees, under this Section 2.4 shall be borne by Pfizer.

2.5. No Implied Rights. Except as expressly provided in this Agreement, neither Party shall be deemed to have granted the other Party (by implication, estoppel or otherwise) any right, title, license or other interest in or with respect to any intellectual property, Know-How or information Controlled by such Party.

2.6. Retained Rights. Pfizer acknowledges that the license rights granted to it under this Agreement are subject to: (a) the rights, conditions and limitations imposed by applicable Law (including 35 U.S.C. § 202 et seq. and regulation pertaining thereto), (b) a non-exclusive royalty-free (as to FSMA) right on the part of FSMA and collaborators of FSMA to practice the Company Patent Rights in the identification, development and commercialization of compounds and therapies for the diagnosis, treatment or prevention of SMA; provided, however, that such compounds are neither Covered by a Valid Claim or [***] nor whose primary or intended mechanism of action is [***], and (c) the Company’s right to perform its obligations hereunder, including under Sections 4.2, 4.3 and 4.4.

2.7. Acknowledgements; Covenants.

2.7.1. Pfizer also acknowledges that the license rights granted to it under this Agreement and its exercise of such license rights are subject to the FSMA-Company Agreement, including Sections 2.1 and 5 thereof, pursuant to which some or all of the intellectual property that is licensed to the Company as of the Effective Date under the FSMA-Company Agreement may become assigned to and owned by the Company in the future. Company covenants to Pfizer that to the extent such intellectual property is not assignable or otherwise is not assigned to the Company, Company will maintain exclusive license rights to such intellectual property such that it continues to be licensed to Pfizer under this Agreement during the Term. Company further covenants to Pfizer that during the Term Company shall maintain (and shall not divest, sell or otherwise transfer) its ownership interests in such intellectual property once the Company becomes the owner of such intellectual property.

2.7.2. Company acknowledges and agrees that Pfizer shall have the right to engage in discussions [***], in each case for the purpose of [***] that may relate to [***], and Company shall cooperate with Pfizer in [***] to the extent reasonably requested by Pfizer; provided however that Pfizer will not have, and will not purport to have, [***].

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

3

EXECUTION VERSION

3. PAYMENTS BY PFIZER TO COMPANY.

3.1. Initial Upfront Payment. In consideration of the execution and delivery of this Agreement, Pfizer shall pay Company a one-time, non-refundable payment of five million dollars ($5,000,000), such amount to be payable within thirty (30) days after the Effective Date. [***] of this one-time upfront payment shall be referred to as a “Tech Transfer Payment.” Company shall use the Tech Transfer Payment in the manner and for the purposes provided for in Section 4.3.3. For avoidance of doubt: (i) Company shall bear the cost of performing its obligations under Section 4.3.3 even if such cost exceeds [***] and (ii) the foregoing initial upfront payment, including the Tech Transfer Payment, shall be non-refundable even if Company’s cost of performing its obligations under Section 4.3.3 are less than [***].

3.2. Clinical and Regulatory Milestones.

3.2.1. In consideration of the execution and delivery of this Agreement, and subject to the provisions of Section 3.2.2, Pfizer shall pay Company the non-refundable amounts set forth below within [***] of the first occurrence of each event described below for the first Licensed Product Covered by a Valid Claim to achieve such event (each, a “Milestone Event”).

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

4

EXECUTION VERSION

	Milestone Event	Milestone Payment
(i)	Successful completion of the Existing Clinical Trial. “Successful completion” means that the drug is generally safe and well-tolerated and that an average [***] of the [***] is achieved after the plasma drug levels reaches steady state at the highest dose tested. In the event that both Parties agree that the Existing Clinical Trial should be terminated prior to completion of the entire study but after the above specified [***] of [***] has been achieved, then [***] of the milestone payment [***] will be paid, and the Parties will then agree in good faith on a definition of successful completion in any additional trial in healthy volunteers in a Licensed Product for the payment of the remaining [***] of the milestone [***]. In the event that Successful completion has been achieved, but only [***] of the [***] has been paid pursuant to the foregoing, then the remainder of this milestone will be payable on that date which is the [***] anniversary of the Effective Date.		[***]
(ii)	Clinical demonstration of increased [***] expression in patients in a Proof of Mechanism PhI Trial (POM). “Clinical demonstration” means that in the Proof of Mechanism PhI Trial (POM) study: The drug is generally safe and well-tolerated with an increase [***]. If Pfizer determines that another biochemical measure is more appropriate for POM, such marker will substitute for [***].		[***]
(iii)	First dosing of first patient in a Proof of Concept Phase Ib Trial of the first Licensed Product.		[***]
(iv)	First dosing of first patient in a Phase IIb/III Clinical Trial of the first Licensed Product.		[***]
(v)	First Commercial Sale of first Licensed Product in the United States.		[***]
(vi)	First Commercial Sale of first Licensed Product in at least two of the following four countries: [***].		[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

5

EXECUTION VERSION

3.2.2. In the event that a Licensed Product for which a Milestone Payment is payable pursuant to this Section 3.2 [***]. Upon achievement of a Milestone Event, Pfizer shall promptly provide written notice to Company informing it of the achievement of such Milestone Event.

[***]

Each of the Milestone Payments set forth above shall be payable one time only (regardless of the number of Licensed Products with respect to which, or the number of times with respect to any Licensed Product, the specified Milestone Event occurs), and only with respect to a Licensed Product Covered by a Valid Claim. No Milestone Payments shall be payable for any subsequent Licensed Product regardless of the number of Licensed Products Developed. For clarification, if one Licensed Product replaces another Licensed Product in Development, such replacement Licensed Product shall only be subject to Milestone Payments that have not previously been triggered by one or more prior Licensed Products.

3.3. Royalty Payments.

3.3.1. Royalties. In consideration of the execution and delivery of this Agreement, Pfizer, on a Licensed Product-by-Licensed Product and country-by-country basis shall pay to Company royalties outlined below in the amount of a percent of the Net Sales in any Pfizer Year during the Royalty Term for such Licensed Product.

Annual Net Sales in the Territory	Royalty Rate
On Pfizer Year Net Sales < [***]		[***]
On additional incremental Pfizer Year Net Sales > [***] and < [***]		[***]
On additional incremental Pfizer Year Net Sales > [***] and < [***]		[***]
On additional incremental Pfizer Year Net Sales > [***]		[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

6

EXECUTION VERSION

3.3.2. Fully Paid-Up, Royalty Free License. Following expiration of the Royalty Term for any Licensed Product in a country, no further royalties shall be payable in respect of sales of such Licensed Product in such country and, thereafter the license granted to Pfizer under Section 2.1 with respect to such Licensed Product in such country shall be a fully paid-up, perpetual, exclusive (even as to Company), irrevocable, royalty-free license.

3.3.3. Royalty Adjustments. The following adjustments shall be made, on a Licensed Product-by-Licensed Product and country-by-country basis, to the royalties payable pursuant to Section 3.3.1, in the following order:

(a) Cessation of [***].

(i) Cessation of [***]. The royalty rate payable pursuant to Section 3.3.1 [***] shall be reduced [***].

(ii) Cessation of [***]. The royalty rate payable pursuant to Section 3.3.1 [***] shall be reduced [***].

(b) Pfizer Agreement [***].

(c) Commercialization of products using the Compound by Third Parties. Royalties payable on Net Sales of a Licensed Product in a country shall be reduced by [***] in respect of Net Sales in any Pfizer Year in any country in which a Third Party commercializes a product using the Compound in an indication outside of SMA in such country.

(d) Generic Entry. Royalties payable on Net Sales of a Licensed Product in a country shall be reduced by [***] in respect of Net Sales in any Pfizer Year in any country in which a Generic Product sold by a Third Party in such country.

(e) Sale of Licensed Product Under Clause (b) of Definition of Royalty Term. Royalties payable on Net Sales of a Licensed Product in a country shall be reduced by [***] in respect of Net Sales in any Pfizer Year in such country at such time that the royalty rate is applicable solely on the basis of clause (b), and not clause (a), of the definition of “Royalty Term.”

(f) Additional Third Party License. If Pfizer determines that it is necessary, desirable or useful to (or it is ordered to or agrees to pay royalties in order to) obtain rights under a Patent Right held by one or more Third Parties [***] in order to research, Develop, Manufacture, Commercialize or use any Licensed Product, whether directly or through any Pfizer Affiliate or Sublicensee, then Pfizer may negotiate and obtain a license under such Patent Right(s) (each such Third Party license referred to herein as an “Additional Third Party License”). Pfizer may reduce the royalties payable under Section 3.3.1 on such

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

7

EXECUTION VERSION

Net Sales by an amount that is equal to [***] of the royalties payable to Third Parties pursuant to any such Additional Third Party Licenses, provided that in no event shall such reductions in the aggregate result in a royalty rate that is less than [***] of the royalty rate which would otherwise be payable in accordance with this Section 3.3 (calculated after application of any and all applicable royalty rate reductions as are set forth in clauses (a) through (e) above).

(g) [***].

(h) [***].

(i) Minimum Royalty. Anything in this Article 3 to the contrary notwithstanding, the royalty payable by Pfizer to the Company in any country in connection with the sale of Licensed Product for any period during the Royalty Term, after giving effect to all reductions and adjustments described in Section 3.3.3(b), (c), (d), (e), (f) and (g) of this Agreement, shall be no less than an amount equal to: [***].

(j) [***].

(k) Company Third Party Agreements. Company shall be solely responsible for all obligations (including any royalty, milestone and other obligations) under its agreements with Third Parties [***] as described in Section 3.3.3(a)(i) in connection with such sales during such period [***], and under [***] as described in Section 3.3.3(a)(ii) in connection with such sales during such period [***]. All such payments shall be made promptly by the Company in accordance with the provisions of all applicable agreements in respect of such intellectual property.

(l) [***].

3.3.4. Method and Manner of Royalty Payment. Royalties shall be calculated as follows:

(a) In calculating the applicable rates in each Pfizer Quarter, the [***] royalty rate will first be calculated based on the cumulative year-to-date aggregate Net Sales in the Territory (for clarity, assuming annual Net Sales of [***], for which [***] of such Net Sales are subject to a royalty rate of [***], and [***] of such Net Sales are subject to a royalty rate of [***], the [***] royalty rate would be calculated as follows: ([***] x [***] plus [***] x [***]) / [***]);

(b) Such [***] royalty rate (the “Average Full Royalty Rate”) will be applied to the cumulative year-to-date Net Sales in any country in which none of the reductions referred to Section 3.3.3 apply;

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

8

EXECUTION VERSION

(c) In respect of all other countries, the Average Full Royalty Rate will then be adjusted for each country after taking into account the reductions referred to in Section 3.3.3. Such adjusted Average Full Royalty Rate will then be applied to the cumulative year-to-date Net Sales in such countries; and

(d) The aggregate royalties payable in each Pfizer Quarter will be the sum of the amounts payable under paragraphs (b) and (c) above, less the aggregate amount of royalties previously paid in respect of such year.

3.3.5. Obligation of the Company to Report to and to Notify Pfizer. For so long as Pfizer is obligated to make royalty payments pursuant to the provisions of this Section 3.3, the Company shall furnish to Pfizer, (i) contemporaneous copies of any royalty or sales reports or other related reports issued or otherwise provided in respect of sales of Licensed Products or payments owing by the Company to [***] under the [***] (as the same are given effect under the FSMA-Company Agreement) or to [***] under the [***] (as the same are given effect under the FSMA-Company Agreement), or, if no such amounts are due or payable under such agreements for any Calendar Quarter, a notice to the effect that no such amounts are due or payable, and (ii) a copy of any and all notices which it receives which relate to any payment obligations (including in respect of royalties or milestones), or which involve an actual, potential or threatened dispute or claim relating to a default under, or termination of, [***].

3.4. Reports and Payments.

3.4.1. Cumulative Royalties. The obligation to pay royalties under this Agreement shall be imposed only once with respect to any sale of any Licensed Product.

3.4.2. Royalty Statements and Payments. Within [***] days of the end of each Calendar Quarter, Pfizer shall deliver to Company a report setting forth for the most recently completed Pfizer Quarter, the following information, on a Licensed Product-by-Licensed Product, country-by-country and Territory-wide basis: (a) gross sales (less returns and on-invoice allowances) of each Licensed Product, (b) deductions from gross sales for each Licensed Product, (c) Net Sales of each Licensed Product, (d) the royalty due hereunder for the sale of each such Licensed Product, and (e) any applicable foreign exchange rates. No such reports shall be due for any such Licensed Product before the First Commercial Sale of such Licensed Product. The total royalty due for the sale of all such Licensed Products during such Pfizer Quarter shall be remitted [***].

3.4.3. Taxes and Withholding. It is understood and agreed between the Parties that any payments made under this Agreement are exclusive of any value added or similar tax (“VAT”), which shall be added thereon as applicable. Where VAT is properly added to a payment made under this Agreement, the Party making the payment will pay the amount of VAT only on receipt of a valid tax invoice issued in accordance

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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with the laws and regulations of the country in which the VAT is chargeable. In addition, in the event any payments made by Pfizer pursuant to this Agreement become subject to withholding taxes under the Laws of any jurisdiction or Governmental Authority, Pfizer shall deduct and withhold the amount of such taxes for the account of Company to the extent required by applicable Law; such amounts payable to Company shall be reduced by the amount of taxes deducted and withheld; and Pfizer shall pay the amounts of such taxes to the proper Governmental Authority in a timely manner and promptly transmit to Company an official tax certificate or other evidence of such tax obligations together with proof of payment from the relevant Governmental Authority of all amounts deducted and withheld sufficient to enable Company to claim such payment of taxes. Any such withholding taxes required under applicable Law to be paid or withheld shall be an expense of, and borne solely by, Company. Pfizer will provide Company with reasonable assistance to enable Company to recover such taxes as permitted by applicable Law.

3.4.4. Currency. All amounts payable and calculations under this Agreement shall be in United States dollars. As applicable, Net Sales and any royalty deductions shall be converted into United States dollars at the exchange rate used by Pfizer for public financial accounting purposes in accordance with GAAP. If, due to restrictions or prohibitions imposed by national or international authority, payments cannot be made as provided in this Section 3, the Parties shall consult with a view to finding a prompt and acceptable solution, and Pfizer will deal with such monies as Company may lawfully direct so long as any action required to be taken by Pfizer is at no additional out-of-pocket expense to Pfizer.

3.4.5. Record Keeping. Pfizer shall keep and shall cause its Affiliates and Sublicensees to keep books and accounts of record in connection with the sale of Licensed Products, in accordance with GAAP and in sufficient detail to permit accurate determination of all figures necessary for verification of royalties to be paid hereunder. Pfizer and its Affiliates shall maintain such records for a period of at least three (3) years after the end of the Pfizer Year in which they were generated.

3.4.6. Audits. Upon [***] days prior notice from Company, Pfizer shall permit an independent certified public accounting firm of nationally recognized standing selected by Company and reasonably acceptable to Pfizer, to examine, at [***], the relevant books and records of Pfizer and its Affiliates as may be reasonably necessary to verify the amounts reported by Pfizer in accordance with Section 3.4.2 and the payment of royalties hereunder. An examination by Company under this Section 3.4.6 shall occur not more than [***] and shall be limited to the pertinent books and records for [***] before the date of the request. The accounting firm shall be provided access to such books and records at Pfizer’s facility(ies) where such books and records are normally kept and such examination shall be conducted during Pfizer’s normal business hours. Pfizer may require the accounting firm to sign a standard non-disclosure agreement before providing the accounting firm access to Pfizer’s facilities or records. Upon completion of the audit, the accounting firm shall provide both Pfizer and Company a written report disclosing any discrepancies in the reports submitted by Pfizer or the royalties paid, and, in each case, the specific details concerning any discrepancies. No other information shall be provided to Company.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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3.4.7. Underpayments/Overpayments. If such accounting firm concludes that additional royalties were due to Company, Pfizer shall pay to Company the additional royalties within [***] days of the date Pfizer receives such accountant’s written report plus interest as set forth in Section 3.4.8. If such accounting firm concludes that Pfizer overpaid royalties to Company, Pfizer shall be entitled to offset such amount against payments that thereafter become due hereunder until such amount has been fully recovered by Pfizer. To the extent not offset, Company will refund such overpayments to Pfizer, within [***] days of the date the Company receives such accountant’s report. Additionally, if the amount of any overpayment or underpayment reported in such audit exceeds [***] of the amount that was properly payable by Pfizer, Pfizer shall reimburse Company for all reasonable charges of such accountants for conducting the audit, but only if and to the extent such overpayment or underpayment was not incurred as a result of any errors or omissions in royalty reports or statements or other documents which were provided by Company to Pfizer, including pursuant to Section 3.3.5.

3.4.8. Late Payments. The payments due to Company under this Agreement shall, if overdue, bear interest beginning on the date on which payment was due and until payment thereof at a per annum rate equal to [***] above the prime rate in effect on the due date as reported by The Wall Street Journal, not to exceed the maximum permitted by law. Any such overdue payments when made shall be accompanied by all interest so accrued. Said interest and the payment and acceptance thereof shall not preclude Company from exercising any other rights it may have as a consequence of the lateness of any payment.

3.4.9. Confidentiality. All reports and financial information of Pfizer which are provided to or subject to review by Company under this Section 3 shall be deemed to be Pfizer’s Confidential Information subject to the provisions of Section 6, and Company shall not disclose such Confidential Information to any Third Party or use such Confidential Information for any purpose other than verifying payments to be made by Pfizer to Company hereunder.

3.5. Pfizer Right of Setoff. If and to the extent Company fails to timely pay FSMA or any Third Party in respect of any payments due in respect of the Company Intellectual Property licensed to Pfizer under this Agreement [***], then Pfizer may, at its election, after reasonable consultation with Company as and to the extent circumstances permit, but otherwise without notice of its election and without demand, (a) pay such payments to FSMA or such Third Party, and (b) charge and setoff such payments against amounts otherwise due from it or its related entities to the Company under this Agreement, and the Company hereby authorizes all

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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such charges and setoffs. Pfizer’s right of set-off as described in this Section 3.5 shall immediately terminate, without any action required by either Party, if and when Pfizer, Company and FSMA enter into an amendment of the FSMA-Company Agreement providing for the Stand-By Rights. “Stand-By Rights” means FSMA, Company and Pfizer will enter into an agreement: (1) to address payment disputes between Company and FSMA, providing for a mechanism for a single set of payments to be made by Pfizer with respect to the portions of payments provided for and which become due under this Agreement that are to be paid on to FSMA, which payments would be made to Company or FSMA (as mutually agreed by such parties) or to a third party escrow agent (if Company and FSMA cannot reach agreement), while also providing for the appropriate portion of such payments to [***]; (2) provided Pfizer makes such payments when due and Pfizer is otherwise not in material breach of this Agreement, then neither Company nor FSMA would challenge or seek to terminate Pfizer’s license rights under the Company Intellectual Property as granted to Pfizer under this Agreement, and Company and FSMA would resolve their disputes without disturbing Pfizer’s license rights; and (3) in the event that Company’s licenses under the FSMA-Company Agreement are terminated for any reason, then, without any action required by any party, Pfizer will have a direct license from FSMA under terms and conditions no less favorable to Pfizer than those set forth in this Agreement, which license would be at least of the same scope sublicensed to Pfizer hereunder, provided that Pfizer is not in material breach of this Agreement or the agreement between FSMA, Company and Pfizer entered into pursuant to the foregoing.

3.6. No Guarantee of Success. Pfizer and Company acknowledge and agree that payments to Company pursuant to Sections 3.2 and 3.3 (i) have been included in this Agreement on the basis that they are only payable or otherwise relevant to the extent that the criteria pursuant to which such payment obligations become payable are satisfied under this Agreement, (ii) as set forth herein are solely intended to allocate amounts that may be achieved upon successful Development or Commercialization, as applicable, of a Licensed Product between Pfizer (who will receive all product sales revenues) and Company, and (iii) will only be triggered, and will only be relevant as provided, in accordance with the terms and conditions of such provisions. Pfizer and Company further acknowledge and agree that nothing in this Agreement will be construed as representing any estimate or projection of (a) the successful Development or Commercialization of any Licensed Product under this Agreement, (b) the number of Licensed Products that will or may be successfully Developed or Commercialized under this Agreement or (c) anticipated sales or the actual value of any Licensed Products that may be successfully Developed or Commercialized under this Agreement. Pfizer makes no representation, warranty or covenant, either express or implied, that (A) it will successfully Develop, Manufacture, Commercialize or continue to Commercialize any Licensed Product in any country, (B) if Commercialized, any Licensed Product will achieve any particular sales level, whether in any individual country or cumulatively throughout the Territory or (C) Pfizer will devote, or cause to be devoted, any level of diligence or resources to Developing, Manufacturing or Commercializing any Licensed Product in any country, or in the Territory in general, other than as expressly required and as provided for under Section 4.5.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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4. TRANSFERS; TRANSITION; PRODUCT DEVELOPMENT, MANUFACTURING AND COMMERCIALIZATION.

4.1. General. Subject to the terms and conditions set forth herein, Pfizer shall have sole authority over and control of the Development, Manufacture, Regulatory Approval and Commercialization throughout the Field of all Compounds and Licensed Products.

4.2. Transfers.

4.2.1. General. As soon as reasonably possible after the Effective Date, but not later than [***], Company, at Company’s cost and expense, shall Successfully transfer to Pfizer the following: (a) tangible embodiments of Company Know-How (all as further set forth in Section 4.2.2 and in technology transfer protocols mutually agreed to by Pfizer and Company technical teams), (b) the Program Materials, (c) the Inventory, and (d) copies of the Program Records. For purposes of this Section 4.2.1 only, “Successfully” means [***].

4.2.2. Disclosure of Technology. As soon as reasonably possible after the Effective Date, but not later than [***], Company, at Company’s cost and expense, shall disclose to Pfizer or its designated Affiliate all Company Know-How that may be necessary or desirable to Pfizer to research, Develop, Manufacture, or Commercialize Licensed Products and efficiently practice the licenses granted to Pfizer under this Agreement [***]. In connection with the foregoing, Company, [***].

4.2.3. Transfer of Regulatory Filings. Company shall promptly deliver or cause to be delivered to Pfizer: all such filings and submissions of Company to the FDA or any other Regulatory Authority, duly executed by Company, as are necessary to effect a transfer of the rights from the Company to Pfizer with respect to all regulatory filings, registrations, authorizations and approvals with or from any Regulatory Authority relating to any of the Compounds and/or Licensed Products, or the Development or Manufacture thereof, to the extent so transferable.

4.2.4. Availability of Records and Personnel. After the Effective Date, Company shall make available to Pfizer and its Affiliates and Representatives during normal business hours when reasonably requested, all Program Records in its possession and shall preserve all such information, records and documents until [***]. Company shall also make available to Pfizer, or cause to be made available to Pfizer, during normal business hours, when reasonably requested, personnel responsible for preparing or maintaining information, records and documents included within the Program Records, or who’s activities relate to the Development of Compounds and/or Licensed Products are the subject of such information, records and documents. Company may continue to use the Retained Information in accordance with the terms of this Agreement.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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4.3. Transition.

4.3.1. General. The Parties desire an efficient, effective transition to Pfizer of ongoing Development, Manufacturing and/or Commercialization activities for the Compounds and Licensed Products that Company has licensed to Pfizer pursuant to Sections 2.1 and 2.2. Company shall cooperate with and provide timely assistance to Pfizer to ensure such transition. To provide for such a transition, the Parties agree to negotiate in good faith and promptly following the Effective Date to enter into a Transition Services Agreement incorporating the terms set forth on Schedule 4.3.1 attached here and such other terms as are mutually agreed by the Parties, and providing for the services specified therein, pursuant to which Company shall perform certain transition services for Pfizer in accordance with the terms and conditions thereof (the “Transition Services Agreement”).

4.3.2. Existing Company Trials. The Transition Services Agreement will provide for the activities the Company will continue to conduct in relation to the completion of Cohort 2 of the Existing Company Trial [***]. As of the Effective Date, with respect to any interactions between Company and any Regulatory Authority for the completion of Cohort 2 of the Existing Company Trial, Pfizer would have: [***].

4.3.3. Company Employees. In support of the activities to be undertaken by Company under Sections 4.2, 4.3.1, this Section 4.3.3 and Section 4.3.4, and in furtherance of the Company’s obligations under Section 4.2.4, Pfizer has provided to Company the Tech Transfer Payment. The Tech Transfer Payment shall be used by Company to support the retention of key employees of Company that have knowledge of the Compounds or Licensed Products that have been Developed to date or the Company Know-How in order to help enable the transfer of such knowledge and Know-How to Pfizer, as provided hereunder. As soon as is practicable following the Effective Date, Representatives of Pfizer and Company shall meet to discuss the transition and the continuing employment by Company of certain employees for purposes of the technology transfer and transition described above. [***]. At all times Company shall remain liable and shall indemnify Pfizer for any and all employment related liabilities associated with Company’s employees, their retention and/or any termination thereof.

4.3.4. [***].

4.4. Manufacturing. In addition to the other provisions of this Section 4, the Company shall provide such consulting services to Pfizer, and the Parties shall cooperate with one another, in respect of the Manufacture of RG 3039 as the Parties may mutually agree, as well as Company providing, at its cost: (a) adequate supply of clinical drug substance to complete the Existing Company Trial, which supply shall consist of not less than [***] (if the Inventory is not sufficient to do this), and (b) for an audit of any Third Party manufacturing facility sites, together with notification to such Third Parties of the right of Pfizer to direct all activities relating to development and manufacturing. For clarity, Pfizer shall have no diligence obligations with respect to the Manufacture of Licensed Products except to the extent necessary to fulfill its obligations pursuant to Section 4.5.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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4.5. Diligence.

4.5.1. Development Diligence. Pfizer shall, directly or indirectly through one or more Sublicensees, use Commercially Reasonable Efforts to develop and commercialize Licensed Products in SMA. For purposes of this Section 4.5, “Commercially Reasonable Efforts” means [***].

4.5.2. Diligence Reports.

(a) Within [***] days after the end of [***] starting from the Effective Date and ending [***] of the Effective Date, Pfizer shall report in writing to Company and FSMA on progress made toward the objectives set forth in Section 4.5.1 during such preceding [***] including progress on research and development, status of applications for regulatory approvals, manufacturing, sublicensing and the number of sublicenses entered into and marketing.

(b) Within [***] days after the end of each [***] commencing [***] of the Effective Date, Pfizer shall report in writing to Company and FSMA on progress made toward the objectives set forth in Section 4.5.1 during such preceding [***] period including progress on research and development, status of applications for regulatory approvals, manufacturing, sublicensing and the number of sublicenses entered into and marketing.

(c) Any information or written report provided by Pfizer to Company pursuant to this Section 4.5.2 shall be deemed to be Pfizer’s Confidential Information and subject to the provisions of Section 6.

4.5.3. [***].

4.5.4. Notification of Diligence Issues. If Company is aware of facts that might form a reasonable basis to allege that Pfizer has failed to meet its obligations under 4.5.1, then Company will promptly notify Pfizer in writing of such potential alleged performance failure (each such potential alleged performance failure, a “Diligence Issue”). [***].

4.5.5. [***].

4.6. Regulatory Approvals. [***]

4.7. Commercialization Activities.

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4.7.1. General. Pfizer shall have sole and exclusive control over all matters relating to the Commercialization of Licensed Products, including sole and exclusive control over (a) pricing of Licensed Products and (b) the negotiation of Licensed Product pricing with Regulatory Authorities and other Third Parties.

4.7.2. Branding. Pfizer or its designated Affiliates or Sublicensees shall select and own all Trademarks used in connection with the Commercialization of any and all Licensed Products. Neither Company nor its Affiliates shall use or seek to register, anywhere in the world, any Trademark which is confusingly similar to any Trademark used by or on behalf of Pfizer, its Affiliates or Sublicensees in connection with any Licensed Product.

4.8. [***].

5. INTELLECTUAL PROPERTY.

5.1. Patent Rights.

5.1.1. Prosecution. Following the Effective Date, Pfizer shall assume responsibility for the preparation, filing, prosecution maintenance and cost of all patent applications and patents included in Company Patent Rights, using patent counsel (outside or internal counsel) and annuity services selected by Pfizer which are reasonably acceptable to FSMA and the Company. The patent counsel and annuity services selected by Pfizer shall utilize any appropriate cost-saving measures in handling filing, prosecution, and maintenance of the patent applications and patents under the Company Patent Rights. Pfizer (through its outside or internal patent counsel) shall promptly provide FSMA and the Company with any and all communications and proposed filings with the United States Patent and Trademark Office, European Patent Office and other foreign equivalents relating to the Company Patent Rights and shall, to the extent practicable, afford FSMA and the Company the opportunity to comment thereon. Pfizer may file a notice with governmental patent offices of the exclusive license to the Company Patent Rights granted to Pfizer hereunder. Pfizer shall have the sole right to file and control any application for patent term extension of any patent that may issue out of Company Patent Rights, based on United States Public Law 98-417 (known as the “Hatch-Waxman Act”) or any equivalent law or regulation in any country under which patent terms may qualify for extension. Company shall supplement and keep up to date Exhibit A throughout the Term. Pfizer shall not have any liability to FSMA and the Company for any act, omission, or default or neglect of outside patent counsel selected pursuant to this Section 5.1.1 by Pfizer with respect to preparing, filing, prosecuting or maintaining Company Patent Rights pursuant to this Section 5.1.1.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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5.1.2. Abandonment by Company. In no event will Company intentionally permit any of the Company Patent Rights to be abandoned in any country nor, if requested by Pfizer to do so, elect not to file a new patent application claiming priority to a patent application within the Company Patent Rights either before such patent application’s issuance or within the time period required for the filing of an international (i.e., Patent Cooperation Treaty), regional (including European Patent Office) or national application, without Pfizer first being given an opportunity to assume responsibility for the continued prosecution and maintenance of such Company Patent Rights or the filing of such new patent application. Accordingly, Company shall provide Pfizer with notice of the allowance and expected issuance date of any patent within the Company Patent Rights, or any of the aforementioned filing deadlines.

5.1.3. Abandonment by Pfizer. Pfizer shall not intentionally permit any of the Company Patent Rights to be abandoned in any country nor, if requested by Company to do so, elect not to file a new patent application claiming priority to a patent application within the Company Patent Rights either before such patent application’s issuance or within the time period required for the filing of an international (i.e., Patent Cooperation Treaty), regional (including European Patent Office) or national application, without Company first being given an opportunity to assume responsibility for the continued prosecution and maintenance of such Company Patent Rights, or the filing of such new patent application. Accordingly, Company shall provide Pfizer with notice of the allowance and expected issuance date of any patent within the Company Patent Rights, or any of the aforementioned filing deadlines.

5.2. Right to Enforce.

5.2.1. In the event that Company or Pfizer becomes aware of a suspected infringement of any Company Patent Right exclusively licensed to Pfizer under this Agreement, such Party shall notify the other Party promptly and confer. Pfizer shall have the right, but shall not be obligated, to bring an infringement action with respect to such infringement at its own expense, in its own name and entirely under its own direction and control, subject to the following or settle any such action, proceeding or dispute, provided that Pfizer considers in good faith any information Company may bring to Pfizer’s attention that public policy or public health concerns may affect the strategy for any such settlement. Company shall reasonably assist Pfizer (at Pfizer’s expense) in any action or proceeding being prosecuted if so requested, and shall not unreasonably withhold consent to lend its name to such actions or proceedings if reasonably requested by Pfizer or required by applicable Law. Company and FSMA shall have the right to participate and be represented in any such suit by its own counsel at its own expense. No settlement of any such action or proceeding which restricts the scope, or adversely affects the enforceability, of a Company Patent Right may be entered into by Pfizer without the prior written consent of Company, which consent shall not be unreasonably withheld.

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5.2.2. If Pfizer fails to initiate an action to abate any alleged infringement of the Company Patent Rights within [***] following the date on which Pfizer first becomes aware of such alleged infringement, or thereafter determines not to maintain such action, FSMA may, upon notice to Pfizer, initiate legal proceedings against the infringer at FSMA’s expense, in its own name and entirely under its own direction and control. Pfizer shall reasonably assist FSMA or its designee (at FSMA’s expense) in any action or proceeding being defended or prosecuted if so requested, and shall lend its name to such actions or proceedings if requested by FSMA or required by applicable law. Pfizer shall have the right to participate and be represented in any such suit by its own counsel at its own expense. No settlement of any such action or proceeding which restricts the scope, or adversely affects the enforceability, of a Company Patent Right may be entered into by FSMA without the prior written consent of Pfizer, which consent shall not be unreasonably withheld by Pfizer. FSMA is an intended third party beneficiary under this section 5.2.2.

5.3. Pfizer Right to Defend. In the event that the validity or scope of any of the Company Patent Rights is challenged by a third party, whether by interference, opposition, reexamination, or any ex parte or inter parte proceeding involving either a patent granting authority or a court of competent jurisdiction; Pfizer shall have the right, but shall not be obligated, to defend the Company Patent Rights against such challenge at its own expense and under its own direction and control. Company shall reasonably assist Pfizer (at Pfizer’s expense) in any action if so requested, and shall have the right to participate in such defense and be represented by counsel of its own selection at its own expense and shall consent to lend its name to such actions or proceedings if reasonably requested by Pfizer or required by applicable Law. Notwithstanding the foregoing, (i) Pfizer shall consult with Company regarding any statements in any written or oral arguments it intends to make in any such action, and shall not make any such statement which Company or its counsel has reasonably determined would detrimentally affect any Company Patent Right or any other patent or patent application owned or controlled by Company; and (ii) Pfizer shall not agree to any settlement of any such action without the prior written consent of Company, such consent not to be unreasonably withheld or delayed. If Pfizer does not take legal action as is required to defend the validity or enforceability of such Company Patent Rights within [***] following the date on which Pfizer first becomes aware of such third party challenge, Pfizer shall provide at least [***] notice to Company prior to a corresponding deadline, if applicable, and Company may then, at its option, assume control and defense of such action at its expense. In the event that Company assumes control of the defense, Pfizer shall give reasonable assistance (excluding financial assistance) to Company. Pfizer may be represented by counsel of its own selection at its own expense in any such legal action, but Company shall have the right to control the action with counsel of its own choice.

5.4. Recovery. Any consideration paid by a third party as the result of proceedings or other actions (whether by way of settlement or otherwise) undertaken by Pfizer pursuant to Section 5.2 above, shall first be applied to reimbursement of the unreimbursed legal fees and expenses reasonably incurred by Pfizer and then the remainder shall be allocated [***] to Pfizer and [***] to Company.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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5.5. Withdrawal. If either Party brings an action or proceeding under this Section 5 and subsequently ceases to pursue or withdraws from such action or proceeding, it shall promptly notify the other Party and the other Party may substitute itself for the withdrawing Party under the terms of this Section 5.

5.6. Recording. If Pfizer deems it necessary or desirable to register or record this Agreement or evidence of this Agreement with any patent office or other appropriate Governmental Authority(ies) in one or more jurisdictions in the Territory, Company shall reasonably cooperate to execute and deliver to Pfizer any documents accurately reflecting or evidencing this Agreement that are necessary or desirable, in Pfizer’s reasonable judgment, to complete such registration or recordation. Pfizer shall reimburse Company for all reasonable out-of-pocket expenses, including attorneys’ fees, incurred by Company in complying with the provisions of this Section 5.6.

6. CONFIDENTIALITY.

6.1. Confidentiality. Except to the extent expressly authorized by this Agreement, the Parties agree that, during the Term and for [***] thereafter, each Party (the “Receiving Party”) receiving any Confidential Information of the other Party (the “Disclosing Party”) hereunder shall: (a) keep the Disclosing Party’s Confidential Information confidential; (b) not disclose, or permit the disclosure of, the Disclosing Party’s Confidential Information; and (c) not use, or permit to be used, the Disclosing Party’s Confidential Information for any purpose other than as expressly permitted under the terms of this Agreement.

6.2. Authorized Disclosure.

6.2.1. Disclosure to Party Representatives. Notwithstanding the foregoing provisions of Section 6.1, the Receiving Party may disclose Confidential Information belonging to the Disclosing Party to the Receiving Party’s Representatives who (a) have a need to know such Confidential Information in connection with the performance of the Receiving Party’s obligations or the exercise of the Receiving Party’s rights under this Agreement and (b) have agreed in writing to non-disclosure and non-use provisions with respect to such Confidential Information that are at least as restrictive as those set forth in this Section 6.

6.2.2. Disclosure to Third Parties. Notwithstanding the foregoing provisions of Section 6.1, each Party may disclose Confidential Information belonging to the other Party to the extent such disclosure is reasonably necessary:

(a) to Governmental Authorities (i) to the extent desirable to obtain or maintain INDs or Regulatory Approvals for any Compound or Licensed Product within the Territory, and (ii) in order to respond to inquiries, requests or investigations relating to Compounds, Licensed Products or this Agreement;

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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(b) to outside consultants, contractors, advisory boards, managed care organizations, and non-clinical and clinical investigators, in each case to the extent desirable to develop, register or market any Compound or Licensed Product; provided that the Receiving Party shall obtain the same confidentiality obligations from such Third Parties as it obtains with respect to its own similar types of confidential information;

(c) in connection with filing or prosecuting Patent Rights or trademark rights as permitted by this Agreement;

(d) in connection with prosecuting or defending litigation as permitted by this Agreement;

(e) subject to the provisions of Section 6.5.2, in connection with or included in scientific presentations and publications relating to Compounds or Licensed Products, including abstracts, posters, journal articles and the like, and posting results of and other information about Clinical Trials to clincialtrials.gov or PhRMA websites;

(f) to the extent necessary or desirable in order to enforce its rights under this Agreement; and

(g) to FSMA to the extent required to perform its obligations under the FSMA-Company Agreement.

If a Party deems it reasonably necessary to disclose Confidential Information belonging to the other Party pursuant to this Section 6.2.2, then the Disclosing Party shall to the extent possible give reasonable advance written notice of such disclosure to the other Party and take such measures to ensure confidential treatment of such information as is reasonably required by the other Party, at the other Party’s expense.

6.3. SEC Filing and Other Disclosures. Either Party may disclose the terms of this Agreement to the extent required, in the reasonable opinion of such Party’s legal counsel, to comply with applicable Law, including the rules and regulations promulgated by the United States Securities and Exchange Commission or any equivalent governmental agency in any country in the Territory. Before disclosing this Agreement or any of the terms hereof pursuant to this Section 6.3, the Parties will consult with one another on the terms of this Agreement to be redacted in making any such disclosure, with the Disclosing Party providing as much advanced notice as is feasible under the circumstances, and giving consideration to the comments of the other Party. Further, if a Party discloses this Agreement or any of the terms hereof in accordance with this Section 6.3, such Party shall, at its own expense, seek such confidential treatment of confidential portions of this Agreement and such other terms, as may be reasonably requested by the other Party.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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6.4. Residual Knowledge Exception. Notwithstanding any provision of this Agreement to the contrary, Residual Knowledge shall not be considered Confidential Information for purposes of this Section 6.

6.5. Public Announcements; Publications.

6.5.1. Announcements. Except as may be expressly permitted under Section 6.3, neither Party will make any public announcement regarding this Agreement without the prior written approval of the other Party. For the sake of clarity, nothing in this Agreement shall prevent Pfizer from making any scientific publication or public announcement with respect to any Licensed Product under this Agreement; provided, however, that, except as permitted under Section 6.2, Pfizer shall not disclose any of Company’s Confidential Information in any such publication or announcement without obtaining Company’s prior written consent to do so. The Parties agree that Company may release the announcement attached hereto as Schedule 6.5.1 regarding the signing of this Agreement following the Effective Date. All public disclosures which are directed toward the Quinazonline/495/RG3039 program shall include a prominent acknowledgement of FSMA similar to the following: “This program was licensed in 2009 from FSMA. FSMA fully funded and directed the preclinical development work with an investment of more than $13 million. It was the very first industrial drug program ever done for SMA.”

6.5.2. Publications. During the Term, each Party shall submit to the other Party (the “Non-Disclosing Party”) for review and approval any proposed academic, scientific and medical publication or public presentation which contains the Non-Disclosing Party’s Confidential Information. In addition, Company shall submit to Pfizer for review and approval any proposed publication or public presentation relating to this Agreement. In both instances, such review and approval will be conducted for the purposes of preserving the value of the Company Intellectual Property and the rights granted to Pfizer hereunder and determining whether any portion of the proposed publication or presentation containing the Non-Disclosing Party’s Confidential Information should be modified or deleted. Written copies of such proposed publication or presentation required to be submitted hereunder shall be submitted to the Non-Disclosing Party no later than [***] before submission for publication or presentation (the “Review Period”). The Non-Disclosing Party shall provide its comments with respect to such publications and presentations within [***] of its receipt of such written copy. The Review Period may be extended for an additional [***] in the event the Non-Disclosing Party can, within [***] of receipt of the written copy, demonstrate reasonable need for such extension including for the preparation and filing of patent applications. Company and Pfizer will each comply with standard academic practice regarding authorship of scientific publications and recognition of contribution of other parties in any publication governed by this Section 6.5.2, including International Committee of Medical Journal Editors standards regarding authorship and contributions. For the sake of clarity, Pfizer’s obligation to submit any publication to Company for review and approval under this Section 6.5.2 shall not apply to any publication which does not contain Company’s Confidential Information.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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7. REPRESENTATIONS AND WARRANTIES.

7.1. Mutual Representations and Warranties. Each of Company and Pfizer hereby represents and warrants to the other Party that:

7.1.1. it is duly organized, validly existing and in good standing under the laws of the jurisdiction of its organization;

7.1.2. the execution, delivery and performance of this Agreement by such Party has been duly authorized by all requisite action under the provisions of its charter, bylaws and other organizational documents, and does not require any action or approval by any of its shareholders or other holders of its voting securities or voting interests;

7.1.3. it has the power and authority to execute and deliver this Agreement and to perform its obligations hereunder;

7.1.4. this Agreement has been duly executed and is a legal, valid and binding obligation on such Party, enforceable against such Party in accordance with its terms; and

7.1.5. the execution, delivery and performance by such Party of this Agreement and its compliance with the terms and provisions hereof does not and will not conflict with or result in a breach of or default under any Binding Obligation existing as of the Effective Date.

7.2. Mutual Covenants. Each of Company and Pfizer hereby covenants to the other Party that, from the Effective Date until expiration or termination of this Agreement, it will perform its obligations under this Agreement in compliance with applicable Laws.

7.3. Representations and Warranties of Company. Company hereby represents and warrants to Pfizer that:

7.3.1. except as expressly disclosed in Schedule 7.3.1, Company is the sole and exclusive owner of the Company Intellectual Property, all of which is free and clear of any claims, liens, charges or encumbrances;

7.3.2. it has and will have the full right, power and authority to grant all of the right, title and interest in the licenses and other rights granted or to be granted to Pfizer, Pfizer’s Affiliates or Pfizer’s Sublicensees under this Agreement;

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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7.3.3. as of the Effective Date (a) Exhibit B sets forth a true and complete list of all Patent Rights owned or otherwise Controlled by Company or its Affiliates that relate to the Compounds or Licensed Products, (b) each such Patent Right remains in full force and effect and (c) Company or its Affiliates have timely paid all filing and renewal fees payable with respect to such Patent Rights;

7.3.4. Exhibit C sets forth a true and complete list of all Compounds discovered or developed by Company or its Affiliates on or prior to the Effective Date;

7.3.5. as of the Effective Date, Company has disclosed to Pfizer all material scientific and technical information and all information relating to safety and efficacy known to it or its Affiliates with respect to the Compounds and Licensed Products;

7.3.6. to its best knowledge, the Company Patent Rights, are, or, upon issuance, will be, valid and enforceable patents and, as of the Effective Date, no Third Party (a) is infringing any Company Patent Right or (b) has challenged or threatened to challenge the scope, validity or enforceability of any Company Patent Right;

7.3.7. it has complied with all applicable Laws, including any disclosure requirements, in connection with the filing, prosecution and maintenance of the Company Patent Rights;

7.3.8. except as expressly disclosed in Schedule 7.3.8, Company has independently developed all Company Know-How or otherwise has a valid right to use, and to permit Pfizer, Pfizer’s Affiliates and Pfizer’s Sublicensees to use, the Company Know-How for all permitted purposes under this Agreement;

7.3.9. neither Company nor any of its Affiliates are party to or otherwise subject to any agreement or arrangement which limits the ownership or licensed rights of Pfizer or its Affiliates with respect to, or limits the ability of Pfizer or its Affiliates to grant a license, sublicense or access, or provide or provide access or other rights in, to or under, any intellectual property right or material (including any Patent Right, Know-How or other data or information), in each case, that would, but for such agreement or arrangement, be included in the rights licensed or assigned to Pfizer or its Affiliates pursuant to this Agreement;

7.3.10. (a) there are no Company Third Party Agreements, other than the Company Third Party Agreements expressly disclosed in Schedule 7.3.10 (each, a “Disclosed Third Party Agreement”), true and complete copies of which have been provided to Pfizer, (b) except as provided in the Disclosed Third Party Agreements, no Third Party has any right, title or interest in or to, or any license under, any Company Intellectual Property, (c) no rights granted by or to Company or its Affiliates or any requirements or obligations set forth under any Disclosed Third Party Agreement conflict

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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with this Agreement or any right or license granted to Pfizer or its Affiliates hereunder, (d) Company and its Affiliates are and at all times have been in compliance in all material respects with all Disclosed Third Party Agreements, and (e) the Disclosed Third Party Agreements are in full force and effect and, to its best knowledge, represent valid and enforceable obligations of the applicable Third Parties party thereto;

7.3.11. to the best of its knowledge, the research, use, Development, Manufacture or Commercialization by Company or Pfizer (or their respective Affiliates or Sublicensees) of any Compound or any Licensed Product (a) does not and will not infringe any issued patent of any Third Party or (b) will not infringe the claims of any published Third Party patent application when and if such claims issue;

7.3.12. there is no (a) claim, demand, suit, proceeding, arbitration, inquiry, investigation or other legal action of any nature, civil, criminal, regulatory or otherwise, pending or, to the best knowledge of Company, threatened against Company or any of its Affiliates or (b) judgment or settlement against or owed by Company or any of its Affiliates, in each case in connection with the Company Intellectual Property, any Compound or any Licensed Product or relating to the transactions contemplated by this Agreement;

7.3.13. no royalty, milestone or other payment are or will become payable to [***] (or any of its assignees or successors) under any agreement entered into by and among FSMA, [***] and Company, other than under the [***], in connection with the Development, Manufacture, Commercialization or use of any Compound or Licensed Product under this Agreement by, on behalf of, or under the authority of, Pfizer;

7.3.14. no royalty, milestone or other payment are due or will ever become due under the [***] in connection with the Development, Manufacture, Commercialization or use of any Compound or Licensed Product under this Agreement by, on behalf of, or under the authority of, Pfizer;

7.3.15. no product sales based royalties are due or will ever become due under the FSMA License Agreement in connection with the Development, Manufacture, Commercialization or use of any Compound or Licensed Product under this Agreement by, on behalf of, or under the authority of, Pfizer;

7.3.16. Conduct of Preclinical and Clinical Trials. (a) Company has heretofore disclosed or otherwise made available to Pfizer all human clinical trials that have been completed or that have otherwise been undertaken by or on behalf of Company with respect to the Licensed Products or Compounds; (b) Company has not received any written notices or other written correspondence from the FDA or any other Governmental Body requiring the termination or suspension of any clinical, pre-clinical, safety or other tests conducted with respect to the Licensed Products or Compounds; and (c) Company is

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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not aware of any pending or threatened potential issuance of any notices or other correspondence from the FDA or any other Governmental Body that would require the termination or suspension of any clinical, pre-clinical, safety or other tests conducted with respect to the Licensed Products or Compounds; and all clinical trials of Licensed Products or Compounds conducted by or on behalf of Company were conducted in material compliance with then-current regulations relating to good clinical practice, the reporting of adverse events, the filing of reports and security promulgated by the FDA and applicable Law;

7.3.17. Clinical Trial Materials. All drug substance (and active pharmaceutical ingredients used therein) administered in human clinical trials by or on behalf of Company with respect to the Licensed Products or Compounds and the Inventory (a) was manufactured in accordance with the applicable specifications and in compliance with the then-applicable good manufacturing practices and applicable Law, (b) was received, stored, handled and processed in accordance with the applicable specifications therefor, (c) met such specifications at the time of use or, with respect to the Inventory, will meet such specifications upon delivery to Pfizer, and (d) with respect to the Inventory and drug substance containing Compound contracted to be delivered to Company from a Third Party, is free and clear of encumbrances; and

7.3.18. Regulatory Correspondence. Company has heretofore disclosed or otherwise made available to Pfizer all material written correspondence: between Company and any Governmental Authorities, between Company and its institutional review boards and drug safety review boards, and between Company and its clinical trial research organization subcontractors, in each case relating to the Licensed Products or Compounds. During the period of time beginning on [***] and continuing until the Effective Date, neither the Company nor its manufacturing subcontractor(s) have received (a) any Form FDA 483 Inspectional Observations or warning letters, (b) any establishment inspection reports or any other documents that indicate or suggest lack of compliance with the regulatory requirements of the FDA or any other Governmental Authority, or (c) equivalents or correspondence similar to any of the foregoing, in each case of (a), (b) and (c) received from the FDA or any other Governmental Authority having jurisdiction over Licensed Products or Compounds and received in relation to Licensed Products or Compounds, or the Manufacture thereof, or received in relation to any facility for the Manufacture of a Licensed Product or Compound or component thereof, (collectively (a), (b) and (c), “Selected Warning Notices”). Company is not aware of any pending or threatened potential issuance of any Selected Warning Notices.

7.4. Company Covenants. In addition to the covenants made by Company elsewhere in this Agreement, Company hereby covenants to Pfizer that, from the Effective Date until expiration or termination of this Agreement:

7.4.1. it shall not, and shall cause its Affiliates not to (a) license, sell, assign or otherwise transfer to any Person (other than Pfizer or its Affiliates or Sublicensees pursuant to the terms of this Agreement) any Company Intellectual Property (or agree to

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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do any of the foregoing) or (b) incur or permit to exist, with respect to any Company Intellectual Property, any lien, encumbrance, charge, security interest, mortgage, liability, assignment, grant of license or other Binding Obligation that is or would be inconsistent with the licenses and other rights granted to Pfizer or its Affiliates under this Agreement;

7.4.2. it will duly perform its obligations and exercise its rights under each Company Third Party Agreement, and it will not take any action, or fail to take any action, under any Company Third Party Agreement that diminishes the rights under the Company Intellectual Property granted to Pfizer under this Agreement;

7.4.3. it will (a) not amend or otherwise modify any Company Third Party Agreement (including any Disclosed Third Party Agreement) or consent or waive rights with respect thereto in any manner that adversely affects (i) the rights granted to Pfizer or Pfizer’s Affiliates or Sublicensees hereunder or (ii) Company’s ability to fully perform its obligations hereunder; (b) promptly furnish Pfizer with true and complete copies of all amendments to the Company Third Party Agreements executed following the Effective Date; (c) remain, and cause its Affiliates to remain, in compliance in all material respects with all Company Third Party Agreements (including Disclosed Third Party Agreements); (d) not terminate, take any action that would result in termination of (or fail to take any action the absence of which would result in termination of) any Disclosed Third Party Agreement; and (e) furnish Pfizer with copies of all notices received by Company or its Affiliates relating to any alleged breach or default by Company or its Affiliates under any Company Third Party Agreement (including any Disclosed Third Party Agreement) within [***] after receipt thereof;

7.4.4. it will not enter into or otherwise allow itself or its Affiliates to be subject to any agreement or arrangement which limits the ownership or licensed rights of Pfizer or its Affiliates with respect to, or limits the ability of Pfizer or its Affiliates to grant a license, sublicense or access, or provide or provide access or other rights in, to or under, any intellectual property right or material (including any Patent Right, Know-How or other data or information), in each case, that would, but for such agreement or arrangement, be included in the rights licensed or assigned to Pfizer or its Affiliates pursuant to this Agreement;

7.4.5. it will maintain valid and enforceable agreements with all Persons acting by or on behalf of Company or its Affiliates under this Agreement which require such Persons to assign to Company their entire right, title and interest in and to all Company Intellectual Property; and

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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7.4.6. it has made or will make any payments owing to any inventor of any Company Intellectual Property or any other Person that is required, in connection with the creation or exploitation of or the transfer of rights to such Company Intellectual Property.

7.5. Representation by Legal Counsel. Each Party hereto represents that it has been represented by legal counsel in connection with this Agreement and acknowledges that it has participated in the drafting hereof. In interpreting and applying the terms and provisions of this Agreement, the Parties agree that no presumption shall exist or be implied against the Party which drafted such terms and provisions.

7.6. Disclaimer. THE FOREGOING REPRESENTATIONS AND WARRANTIES OF EACH PARTY ARE IN LIEU OF ANY OTHER REPRESENTATIONS AND WARRANTIES, EXPRESS OR IMPLIED, INCLUDING ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR ANY IMPLIED WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE, ALL OF WHICH ARE HEREBY SPECIFICALLY EXCLUDED AND DISCLAIMED.

8. TERM AND TERMINATION.

8.1. Term. The term of this Agreement (the “Term”) will commence on the Effective Date and extend on a country-by-country basis (in the Territory), unless this Agreement is terminated earlier in accordance with this Section 8, until the last to expire of any Royalty Term for any Licensed Product in such country in the Territory.

8.2. Termination by Company. Company may terminate this Agreement for cause, at any time during the Term, by giving written notice to Pfizer in the event that Pfizer commits a material breach of its obligations under this Agreement and such material breach remains uncured for [***], measured from the date written notice of such material breach is given to Pfizer. If the alleged material breach relates to non-payment of any amount due under this Agreement, the cure period shall be [***].

8.3. Termination by Pfizer.

8.3.1. Termination for Convenience. Upon at least [***] written notice to Company, Pfizer may terminate this Agreement on a Licensed Product-by-Licensed Product and country-by-country basis, or in its entirety, without cause, for any or no reason.

8.3.2. Termination for Cause. Pfizer may terminate this Agreement in its entirety for cause , at any time during the Term, by giving written notice to Company in the event that Company commits a material breach of its obligations under this Agreement and such material breach remains uncured for [***], measured from the date written notice of such material breach is given to Company.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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8.4. Termination of FSMA-Company Agreement. This Agreement shall terminate upon the termination of the FSMA-Company Agreement. Company hereby covenants that: (a) it will not terminate the FSMA-Company Agreement and (b) it will give prompt written notice to Pfizer of (i) the occurrence of any event that constitutes a breach of the FSMA-Company Agreement by either party thereto or (ii) the receipt of notice of breach or termination by the Company from FSMA.

8.5. Effects of Termination.

8.5.1. Effect of Termination.

(a) Termination Generally. Upon termination of this Agreement for any reason, final reports in accordance with Section 3.4 shall be submitted to the Company. The termination or expiration of this Agreement or any licenses granted hereunder shall not relieve Pfizer, or any of its Affiliates or Sublicensees, of any obligations arising before such termination or expiration.

(b) Termination prior to the Trigger Date. In the event that this Agreement is terminated prior to the Trigger Date other than in the event of a breach by the Company, then (except as otherwise expressly provided in this Agreement, including Section 8.5.2), (A) Pfizer and Company shall negotiate in good faith the reversion of all rights, including license rights, in respect of Company Intellectual Property from Pfizer to Company and all preclinical, clinical, manufacturing data and regulatory filings owned or controlled by Pfizer with respect to each Licensed Product, but only to the extent not related to any Compounds or other subject matter owned by Pfizer or licensed to Pfizer by Third Parties; (B) Company shall, within [***] following the effective date of termination, deliver to Pfizer all Confidential Information received hereunder; and (C) except as otherwise expressly provided herein, all other rights and obligations of each Party with respect to all Licensed Products throughout the Territory shall cease.

(c) Other Effects of Termination. Upon termination (but not expiration) of this Agreement for any reason following the Trigger Date, the following shall apply at the request of Company:

(i) Pfizer shall promptly: (i) disclose and transfer to Company a true and complete copy of all preclinical, clinical and manufacturing data owned or controlled by Pfizer with respect to each Licensed Product, (ii) authorize Company or its designees to reference all drug master files

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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owned or controlled by Pfizer with respect to each Licensed Product, and (iii) assign to Company or its designees ownership of all regulatory filings made by or on behalf of Pfizer with respect to any Licensed Product. Company agrees to pay to Pfizer a royalty fee of [***] of Net Sales of those Licensed Products on which Company would be required to pay [***] a royalty capped at the [***] (the data, right of reference and assignment of regulatory filings are the “Reversion Rights”). As used in this Section only, “Net Sales” shall mean the total gross amount invoiced on the sale of Licensed Product by Company and its sublicensees to third parties, less the following items: [***]. In the event that Company or its sublicensees receives, in any transaction included within the definition of Net Sales, any non-cash compensation or lower prices on other products in exchange for any Licensed Products, or sells Licensed Products in other than an arms-length transaction, then for the purposes of determining Net Sales hereunder the gross amount invoiced in such transaction shall be deemed to be the gross amount that would have been paid had there been such a sale at the average sale price of such Licensed Products during the applicable royalty reporting period in the country in which such disposition took place or, if such amount cannot be determined, the average sales price of such Licensed Products in those countries in which Licensed Products are then being marketed. The preceding sentence shall not apply to the distribution at no cost of Licensed Products to physicians, hospitals or clinics for promotional purposes or academic investigators for research and clinical trial purposes, which are not included in the definition of Net Sales. In the event that Licensed Products are sold in combination with one or more other therapeutically active prescription pharmaceutical ingredient (each such ingredient being an “Active Ingredient”), the Net Sales on the combination product shall be calculated [***].

8.5.2. Accrued Rights. Expiration or termination of this Agreement for any reason shall be without prejudice to any right which shall have accrued to the benefit of either Party prior to such termination, including damages arising from any breach under this Agreement. Expiration or termination of this Agreement shall not relieve either Party from any obligation which is expressly indicated to survive such expiration or termination.

8.5.3. Survival Period. The following sections, together with any sections that expressly survive (including any perpetual licenses granted hereunder), shall survive expiration or termination of this Agreement for any reason: Sections 1 and Exhibit A (Definitions and Interpretation), 2.2 (Non-Exclusive Licenses from Company to Pfizer), 3.3.2 (Fully Paid-Up Royalty Free License) (upon expiration of this Agreement only), 3.3.3(k) (Company Third Party Agreements), 4.5.5 (Safety or Efficacy Issues), 4.8 (Other

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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Pfizer Programs), 6 (Confidentiality) (for [***] years following the expiration or termination of this Agreement, except for Section 6.5.2, which shall survive), 7 (Representations and Warranties), (8.5 (Effects of Termination), 8.6 (Provision for Insolvency), 9.1 (No Consequential Damages), 9.2 (Indemnification by Pfizer), 9.3 (Indemnification by Company), 9.4 (Procedure), and 10 (Miscellaneous).

8.6. Provision for Insolvency.

8.6.1. Termination Right. Company shall be deemed a “Debtor” under this Agreement if, at any time during the Term (a) a case is commenced by or against Company under the Bankruptcy Code, (b) Company files for or is subject to the institution of bankruptcy, reorganization, liquidation or receivership proceedings (other than a case under the Bankruptcy Code), (c) Company assigns all or a substantial portion of its assets for the benefit of creditors, (d) a receiver or custodian is appointed for Company’s business or (e) a substantial portion of Company’s business is subject to attachment or similar process; provided, however, that in the case of any involuntary case under the Bankruptcy Code, Company shall not be deemed a Debtor if the case is dismissed within 60 days after the commencement thereof. If Company is deemed a Debtor, then Pfizer may terminate this Agreement by providing written notice to Company.

8.6.2. Rights to Intellectual Property. All rights and licenses now or hereafter granted by Company to Pfizer under or pursuant to any Section of this Agreement, including Sections 2.1, 2.2 and 4.2 hereof, are rights to “intellectual property” (as defined in the Bankruptcy Code). The Parties hereto acknowledge and agree that the payments provided for under Section 3 and any other payments by Pfizer to Company hereunder, other than royalty payments pursuant to Section 3.3, do not constitute royalties within the meaning of Section 365(n) of the Bankruptcy Code or relate to licenses of intellectual property hereunder. If (a) a case under the Bankruptcy Code is commenced by or against Company, (b) this Agreement is rejected as provided in the Bankruptcy Code and (c) Pfizer elects to retain its rights hereunder as provided in Section 365(n) of the Bankruptcy Code, then Company (in any capacity, including debtor-in-possession) and its successors and assigns (including any trustee) shall provide to Pfizer all intellectual property licensed hereunder. Company shall not interfere with the exercise by Pfizer or its Affiliates of rights and licenses to intellectual property licensed hereunder and embodiments thereof in accordance with this Agreement and agrees to use commercially reasonable efforts to assist Pfizer and its Affiliates to obtain such intellectual property and embodiments thereof in the possession or control of Third Parties as reasonably necessary or desirable for Pfizer or its Affiliates or Sublicensees to exercise such rights and licenses in accordance with this Agreement.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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8.6.3. No Limitation of Rights. All rights, powers and remedies of Pfizer provided in this Section 8.6 are in addition to and not in substitution for any and all other rights, powers and remedies now or hereafter existing at Law or in equity (including the Bankruptcy Code) in the event of the commencement of a case under the Bankruptcy Code involving Company.

9. LIMITATION ON LIABILITY, INDEMNIFICATION AND INSURANCE.

9.1. No Consequential Damages. Except with respect to liability arising from a breach of Section 5 or 6, from any willful misconduct or intentionally wrongful act, or to the extent such Party may be required to indemnify the other Party under this Section 9, in no event will either Party or its Representatives be liable under this Agreement for any special, indirect, incidental, consequential or punitive damages, whether in contract, warranty, tort, negligence, strict liability or otherwise, including loss of profits or revenue suffered by either Party or any of its Representatives. Without limiting the generality of the foregoing, “consequential damages” will be deemed to include, and neither Party will be liable to the other Party or any of such other Party’s Representatives or stockholders for any damages based on or measured by loss of projected or speculative future sales of the Licensed Products, any Milestone Payment due upon any unachieved Milestone Event under Section 3.2, any unearned royalties under Section 3.3 or any other unearned, speculative or otherwise contingent payments provided for in this Agreement.

9.2. Indemnification by Pfizer. Pfizer will indemnify, defend and hold harmless Company, each of its Affiliates, and each of its and its Affiliates’ employees, officers, directors and agents (each, a “Company Indemnified Party”) from and against any and all liability, loss, damage, expense (including reasonable attorneys’ fees and expenses) and cost (collectively, a “Liability”) that the Company Indemnified Party may be required to pay to one or more Third Parties resulting from or arising out of:

(a) Development, Manufacture, Commercialization or use of any Compound or Licensed Product by, on behalf of, or under the authority of, Pfizer (other than by any Company Indemnified Party); or

(b) the material breach by Pfizer of any of its representations, warranties or covenants set forth in this Agreement;

except, in each case, to the extent caused by the negligence, recklessness or intentional acts of Company or any Company Indemnified Party and claims for which Company is required to indemnify Pfizer pursuant to Section 9.3.

9.3. Indemnification by Company. Company will indemnify, defend and hold harmless Pfizer, its Affiliates, Sublicensees, contractors, distributors and each of its and their respective employees, officers, directors and agents (each, a “Pfizer Indemnified Party”) from and against any and all Liabilities that the Pfizer Indemnified Party may be required to pay to one or more Third Parties resulting from or arising out of:

(a) Development, Manufacture, Commercialization or use of any compound or product pursuant to the exercise of the Reversion Rights by, on behalf of, or under the authority of, Company;

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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(b) the material breach by Company of any of its representations, warranties or covenants set forth in this Agreement; or

(c) any claim relating to Company’s Development of Licensed Product in Cohort 1 or Cohort 2 of the Existing Company Trial.

except to the extent caused by the negligence, recklessness or intentional acts of Pfizer or any Pfizer Indemnified Party and claims for which Pfizer is required to indemnify Company pursuant to Section 9.2.

9.4. Procedure.

9.4.1. Notice. Each Party will notify the other Party in writing in the event it becomes aware of a claim for which indemnification may be sought hereunder. In the event that any Third Party asserts a claim or other proceeding (including any governmental investigation) with respect to any matter for which a Party (the “Indemnified Party”) is entitled to indemnification hereunder (a “Third Party Claim”), then the Indemnified Party shall promptly notify the Party obligated to indemnify the Indemnified Party (the “Indemnifying Party”) thereof; provided, however, that no delay on the part of the Indemnified Party in notifying the Indemnifying Party shall relieve the Indemnifying Party from any obligation hereunder unless (and then only to the extent that) the Indemnifying Party is prejudiced thereby.

9.4.2. Control. Subject to Pfizer’s right to control any actions described in Section 5 (even where Company is the Indemnifying Party), the Indemnifying Party shall have the right, exercisable by notice to the Indemnified Party within [***] after receipt of notice from the Indemnified Party of the commencement of or assertion of any Third Party Claim, to assume direction and control of the defense, litigation, settlement, appeal or other disposition of the Third Party Claim (including the right to settle the claim solely for monetary consideration) with counsel selected by the Indemnifying Party and reasonably acceptable to the Indemnified Party; provided that (a) the Indemnifying Party has sufficient financial resources, in the reasonable judgment of the Indemnified Party, to satisfy the amount of any adverse monetary judgment that is sought, (b) the Third Party Claim seeks solely monetary damages and (c) the Indemnifying Party expressly agrees in writing that as between the Indemnifying Party and the Indemnified Party, the Indemnifying Party shall be solely obligated to satisfy and discharge the Third Party Claim in full (the conditions set forth in clauses (a), (b) and (c) above are collectively referred to as the “Litigation Conditions”). Within [***] after the Indemnifying Party has given notice to the Indemnified Party of its exercise of its right to defend a Third Party

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

Claim, the Indemnified Party shall give notice to the Indemnifying Party of any objection thereto based upon the Litigation Conditions. If the Indemnified Party reasonably so objects, the Indemnified Party shall continue to defend the Third Party Claim, at the expense of the Indemnifying Party, until such time as such objection is withdrawn. If no such notice is given, or if any such objection is withdrawn, the Indemnifying Party shall be entitled, at its sole cost and expense, to assume direction and control of such defense, with counsel selected by the Indemnifying Party and reasonably acceptable to the Indemnified Party. During such time as the Indemnifying Party is controlling the defense of such Third Party Claim, the Indemnified Party shall cooperate, and shall cause its Affiliates and agents to cooperate upon request of the Indemnifying Party, in the defense or prosecution of the Third Party Claim, including by furnishing such records, information and testimony and attending such conferences, discovery proceedings, hearings, trials or appeals as may reasonably be requested by the Indemnifying Party. In the event that the Indemnifying Party does not satisfy the Litigation Conditions or does not notify the Indemnified Party of the Indemnifying Party’s intent to defend any Third Party Claim within [***] after notice thereof, the Indemnified Party may (without further notice to the Indemnifying Party) undertake the defense thereof with counsel of its choice and at the Indemnifying Party’s expense (including reasonable, out-of-pocket attorneys’ fees and costs and expenses of enforcement or defense). The Indemnifying Party or the Indemnified Party, as the case may be, shall have the right to join in (including the right to conduct discovery, interview and examine witnesses and participate in all settlement conferences), but not control, at its own expense, the defense of any Third Party Claim that the other party is defending as provided in this Agreement.

9.4.3. Settlement. The Indemnifying Party shall not, without the prior written consent of the Indemnified Party, enter into any compromise or settlement that commits the Indemnified Party to take, or to forbear to take, any action. The Indemnified Party shall have the sole and exclusive right to settle any Third Party Claim, on such terms and conditions as it deems reasonably appropriate, to the extent such Third Party Claim involves equitable or other non-monetary relief, but shall not have the right to settle such Third Party Claim to the extent such Third Party Claim involves monetary damages without the prior written consent of the Indemnifying Party. Each of the Indemnifying Party and the Indemnified Party shall not make any admission of liability in respect of any Third Party Claim without the prior written consent of the other party, and the Indemnified Party shall use reasonable efforts to mitigate Liabilities arising from such Third Party Claim.

9.5. Insurance. Each Party further agrees to obtain and maintain, during the Term, commercial general liability insurance, including products liability insurance, with reputable and financially secure insurance carriers (or pursuant to a program of self-insurance reasonably satisfactory to the other Party) to cover its indemnification obligations under Section 9.2 or Section 9.3, as applicable, [***].

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

10. MISCELLANEOUS.

10.1. Assignment. Neither this Agreement nor any interest hereunder shall be assignable by a Party without the prior written consent of the other Party, except as follows: (a) a Party may assign its rights and obligations under this Agreement by way of sale of itself or the sale of the portion of its business to which this Agreement relates, through merger, sale of assets and/or sale of stock or ownership interest, provided that the assignee shall expressly agree to be bound by the applicable obligations of such Party under this Agreement and that such sale is not primarily for the benefit of its creditors, (b) such Party may assign its rights and obligations under this Agreement to any of its Affiliates, provided that the assignee shall expressly agree to be bound by the applicable obligations of such Party under this Agreement and that such Party shall remain liable for all of its rights and obligations under this Agreement. In addition, Pfizer may assign its rights and obligations under this Agreement to a Third Party where Pfizer or its Affiliate is required, or makes a good faith determination based on advice of counsel, to divest a Licensed Product in order to comply with Law or the order of any Governmental Authority as a result of a merger or acquisition, provided that the assignee shall expressly agree to be bound by Pfizer’s obligations under this Agreement. Each Party shall promptly notify the other Party of any assignment or transfer (other than to an Affiliate) under the provisions of this Section 10.1. This Agreement shall be binding upon the successors and permitted assigns of the Parties and the name of a Party appearing herein shall be deemed to include the names of such Party’s successors and permitted assigns to the extent necessary to carry out the intent of this Agreement. Any assignment not in accordance with this Section 10.1 shall be void.

10.2. Further Actions. Each Party agrees to execute, acknowledge and deliver such further instruments, and to do all such other acts, as may be necessary or appropriate in order to carry out the purposes and intent of the Agreement.

10.3. Force Majeure. Each Party shall be excused from the performance of its obligations under this Agreement to the extent that such performance is prevented by force majeure (defined below) and the nonperforming Party promptly provides notice of the prevention to the other Party. Such excuse shall be continued so long as the condition constituting force majeure continues and the nonperforming Party takes Commercially Reasonable Efforts to remove the condition. For purposes of this Agreement, “force majeure” shall include conditions beyond the control of the Parties, including an act of God, voluntary or involuntary compliance with any regulation, Law or order of any government, war, act of terror, civil commotion, labor strike or lock-out, epidemic, failure or default of public utilities or common carriers, destruction of production facilities or materials by fire, earthquake, storm or like catastrophe.

10.4. Notices. Any notice or notification required or permitted to be provided pursuant to the terms and conditions of this Agreement (including any notice of force majeure, breach, termination, change of address, etc.) shall be in writing and shall be deemed given upon receipt if delivered personally or by facsimile transmission (receipt verified), five days after deposited in the mail if mailed by registered or certified mail (return receipt requested) postage

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

prepaid, or on the next Business Day if sent by overnight delivery using a nationally recognized express courier service and specifying next Business Day delivery (receipt verified), to the Parties at the following addresses or facsimile numbers (or at such other address or facsimile number for a Party as shall be specified by like notice; provided, however, that notices of a change of address shall be effective only upon receipt thereof):

All correspondence to Pfizer shall be addressed as follows:

Pfizer - Notices:	Pfizer Inc. Notices: R&D Business Development 235 East 42nd Street New York, NY 10017 Attn.: R&DBD Contract Notice
with copy to:	Pfizer Inc. Notices: Pfizer Legal Division 235 East 42nd Street New York, NY 10017 Attn.: Chief Counsel, R&D Fax: +1-646-563-9619

To help expedite our awareness and response, copies of notices may be provided by to Pfizer by email but must be supplemented by one of the following methods (a) personal delivery; (b) first class certified mail with return receipt requested, or (c) next-day delivery by major international courier, with confirmation of delivery. Electronic copies may be sent to contractnotices@pfizer.com.

All correspondence to Company shall be addressed as follows:

	Repligen Corporation 41 Seyon Street Building #1, Suite 100 Waltham, MA 02453 Attn.: Chief Executive Officer Fax: (781) 250-0115
with a copy to:	Goodwin Procter Exchange Place Boston, MA 02109 Attn.: Christopher Denn Fax: (617) 523-1231

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

10.5. Amendment. No amendment, modification or supplement of any provision of this Agreement shall be valid or effective unless made in writing and signed by a duly authorized officer of each Party.

10.6. Waiver. No provision of this Agreement shall be waived by any act, omission or knowledge of a Party or its agents or employees except by an instrument in writing expressly waiving such provision and signed by a duly authorized officer of the waiving Party. The waiver by either of the Parties of any breach of any provision hereof by the other Party shall not be construed to be a waiver of any succeeding breach of such provision or a waiver of the provision itself.

10.7. Severability. If any clause or portion thereof in this Agreement is for any reason held to be invalid, illegal or unenforceable, the same shall not affect any other portion of this Agreement, as it is the intent of the Parties that this Agreement shall be construed in such fashion as to maintain its existence, validity and enforceability to the greatest extent possible. In any such event, this Agreement shall be construed as if such clause of portion thereof had never been contained in this Agreement, and there shall be deemed substituted therefor such provision as will most nearly carry out the intent of the Parties as expressed in this Agreement to the fullest extent permitted by applicable Law.

10.8. Descriptive Headings. The descriptive headings of this Agreement are for convenience only and shall be of no force or effect in construing or interpreting any of the provisions of this Agreement.

10.9. Export Control. This Agreement is made subject to any restrictions concerning the export of products or technical information from the United States of America or other countries which may be imposed upon or related to Company or Pfizer from time to time. Each Party agrees that it will not export, directly or indirectly, any technical information acquired from the other Party under this Agreement or any products using such technical information to a location or in a manner that at the time of export requires an export license or other governmental approval, without first obtaining the written consent to do so from the appropriate agency or other governmental entity.

10.10. Dispute Resolution. If any dispute or disagreement arises between Pfizer and Company in respect of this Agreement, they shall follow the following procedures in an attempt to resolve the dispute or disagreement:

10.10.1. The Party claiming that such a dispute exists shall give notice in writing (“Notice of Dispute”) to the other Party of the nature of the dispute.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

10.10.2. Within [***] of receipt of a Notice of Dispute, the Senior Vice President Global Operations of Company and the Group SVP for Biotherapeutics Research and Development of Pfizer shall meet in person or by teleconference and exchange written summaries reflecting, in reasonable detail, the nature and extent of the dispute, and at this meeting they shall use their reasonable endeavors to resolve the dispute.

10.10.3. If, within [***] of initial receipt of the Notice of Dispute, the dispute has not been resolved, then the Parties agree that either Party may initiate litigation to resolve the dispute.

Notwithstanding any provision of this Agreement to the contrary, either Party may immediately initiate litigation in any court set forth in Section 10.12 seeking any remedy at law or in equity, including the issuance of a preliminary, temporary or permanent injunction, to preserve or enforce its rights under this Agreement. The provisions of this Section 10.10 will survive for [***] years from the date of termination or expiration of this Agreement.

10.11. Governing Law. This Agreement, and all claims arising under or in connection therewith, shall be governed by and interpreted in accordance with the substantive laws of the State of New York, without regard to conflict of law principles thereof.

10.12. Consent to Jurisdiction. Each Party to this Agreement hereby (a) irrevocably submits to the exclusive jurisdiction of the United States District Court for the Southern District of New York or, if such court does not have subject matter jurisdiction, the state courts of the State of New York, for the purpose of any and all actions, suits or proceedings arising in whole or in part out of, related to, based upon or in connection with this Agreement or the subject matter hereof, (b) waives to the extent not prohibited by applicable Law, and agrees not to assert, by way of motion, as a defense or otherwise, in any such action, any claim that it is not subject personally to the jurisdiction of the above-named courts, that its property is exempt or immune from attachment or execution, that any such action brought in one of the above-named courts should be dismissed on grounds of forum non conveniens, should be transferred to any court other than one of the above-named courts, or should be stayed by reason of the pendency of some other proceeding in any other court other than one of the above-named courts, or that this Agreement or the subject matter hereof may not be enforced in or by such court, and (c) agrees not to commence any such action other than before one of the above-named courts nor to make any motion or take any other action seeking or intending to cause the transfer or removal of any such action to any court other than one of the above-named courts whether on the grounds of inconvenient forum or otherwise.

10.13. Entire Agreement. This Agreement constitutes and contains the complete, final and exclusive understanding and agreement of the Parties and cancels and supersedes any and all prior negotiations, correspondence, understandings and agreements, whether oral or written, between the Parties respecting the subject matter hereof and thereof, including that certain Confidential Disclosure Agreement between the Parties dated [***], as amended on [***], which is hereby terminated effective as of the Effective Date.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

10.14. Independent Contractors. Both Parties are independent contractors under this Agreement. Nothing herein contained shall be deemed to create an employment, agency, joint venture or partnership relationship between the Parties hereto or any of their agents or employees, or any other legal arrangement that would impose liability upon one Party for the act or failure to act of the other Party. Neither Party shall have any express or implied power to enter into any contracts or commitments or to incur any liabilities in the name of, or on behalf of, the other Party, or to bind the other Party in any respect whatsoever.

10.15. Counterparts. This Agreement may be executed in two counterparts, each of which shall be an original and both of which shall constitute together the same document. Counterparts may be signed and delivered by facsimile or PDF file, each of which shall be binding when received by the applicable Party.

10.16. No Third Party Rights or Obligations. No provision of this Agreement shall be deemed or construed in any way to result in the creation of any rights or obligation in any Person not a Party to this Agreement. However, Pfizer may decide, in its sole discretion, to use one or more of its Affiliates to perform its obligations and duties hereunder, provided that Pfizer shall remain liable hereunder for the performance by any such Affiliates of any such obligations.

(Signature page follows.)

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

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EXECUTION VERSION

IN WITNESS WHEREOF, authorized representatives of the Parties have duly executed this Agreement as of the Effective Date to be effective as of the Effective Date.

PFIZER INC		REPLIGEN CORPORATION
By	/s/ Mikael Dolsten	By	/s/ Walter C. Herlihy
Name:	Mikael Dolsten	Name:	Walter C. Herlihy
Title:	President – Worldwide R&D	Title:	President & Chief Executive Officer

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Signature Page to License Agreement

EXECUTION VERSION

Exhibit A

Defined Terms

“[***] and FSMA License Agreement” means the License Agreement between [***] and FSMA dated [***], as amended, which has been terminated pursuant to such agreement and subsequent correspondence.

“Affiliate” means, as of any point in time and for so long as such relationship continues to exist with respect to any Person, any other Person that controls, is controlled by or is under common control with such Person. A Person shall be regarded as in control of another Person if it (a) owns or controls at least fifty (50%) of the equity securities of the subject Person entitled to vote in the election of directors or (b) possesses, directly or indirectly, the power to direct or cause the direction of the management or policies of any such Person (whether through ownership of securities or other ownership interests, by contract or otherwise).

“Bankruptcy Code” means Section 101(35A) of Title 11 of the United States Code, as amended.

“Binding Obligation” means, with respect to a Party (a) any oral or written agreement or arrangement that binds or affects such Party’s operations or property, including any assignment, license agreement, loan agreement, guaranty, or financing agreement, (b) the provisions of such Party’s charter, bylaws or other organizational documents or (c) any order, writ, injunction, decree or judgment of any court or Governmental Authority entered against such Party or by which any of such Party’s operations or property are bound.

“Biomarker Trial” means a trial that does not measure functional endpoints that demonstrate patient improvement.

“Business Day” means a day other than a Saturday, Sunday or bank or other public holiday in New York, New York.

“Calendar Quarter” means the respective periods of three (3) consecutive calendar months ending on March 31, June 30, September 30 or December 31, for so long as this Agreement is in effect.

“Calendar Year” means any calendar year.

“Clinical Trial” means a human clinical study conducted on sufficient numbers of human subjects that is designed to (a) establish that a pharmaceutical product is reasonably safe for continued testing, (b) investigate the safety and efficacy of the pharmaceutical product for its intended use, and to define warnings, precautions and adverse reactions that may be associated with the pharmaceutical product in the dosage range to be prescribed or (c) support Regulatory

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-2

EXECUTION VERSION

Approval of such pharmaceutical product or label expansion of such pharmaceutical product. Without limiting the foregoing, Clinical Trial includes any Phase I Clinical Trial, Phase Ib Clinical Trial, Phase IIb/III Clinical Trial, Proof of Concept Phase Ib Trial or Proof of Mechanism PhI Trial (POM).

“Cohort 1” means the dosing of subjects identified as “Cohort 1” as described in protocol [***], Dated [***].

“Cohort 2” means the dosing of subjects identified as “Cohort 2” as described in protocol [***], Dated [***].

“Combination Product” means any Licensed Product containing as active pharmaceutical ingredients both (a) a Compound and (b) one or more pharmaceutically active compounds or substances that are not a Compound.

“Commercialize” or “Commercializing” means to market, promote, distribute, offer for sale, sell, have sold, import, have imported, export, have exported or otherwise commercialize a compound or product. When used as a noun, “Commercialization” means any and all activities involved in Commercializing.

“Company Intellectual Property” means Company Patent Rights and Company Know-How.

“Company Know-How” means [***].

“Company Patent Right” means any Patent Right that [***].

“Company Third Party Agreement” means any agreement between Company (or any of its Affiliates) and any Third Party that relates to any of the Company Intellectual Property.

“Compound” means (i) RG 3039, [***].

“Confidential Information” means, with respect to each Party, all Know-How or other information, including proprietary information and materials (whether or not patentable) regarding or embodying such Party’s technology, products, business information or objectives, that is communicated by or on behalf of the Disclosing Party to the Receiving Party or its permitted recipients, on or after the Effective Date. Confidential Information does not include any Know-How or other information that (a) was already known by the Receiving Party (other than under an obligation of confidentiality to the Disclosing Party) at the time of disclosure by or on behalf of the Disclosing Party, (b) was generally available to the public or otherwise part of the public domain at the time of its disclosure to the Receiving Party, (c) became generally available to the public or otherwise part of the public domain after its disclosure to the Receiving Party, other than through any act or omission of the Receiving Party in breach of its obligations under this Agreement, (d) was disclosed to the Receiving Party, other than under an obligation of

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-3

EXECUTION VERSION

confidentiality, by a Third Party who had no obligation to the Disclosing Party not to disclose such information to the Receiving Party or (e) was independently discovered or developed by or on behalf of the Receiving Party without the use of any Confidential Information belonging to the Disclosing Party. The terms and conditions of this Agreement shall be considered Confidential Information of both Parties.

“Control” or “Controlled” when used in reference to intellectual property or intellectual property rights, means the legal authority or right, by virtue of ownership, license or otherwise, of a Party to grant a license or sublicense of such intellectual property rights to the other Party.

“Covered by” means, with reference to a particular Licensed Product, that the sale, importation or use of such Licensed Product by a party that does not own or have rights to the relevant Patent, would infringe a Valid Claim of the relevant Patent in the country in which such activity occurs.

“DcpS” means Scavenger Decapping Enzyme DcpS.

“[***]” means [***]

“[***] Agreement” means the Assignment Agreement dated [***] between FSMA and [***].

“[***] Assigned Patent Right” means any Patent Right assigned to FSMA by [***] under the [***].

“Develop” or “Developing” means to discover, research or otherwise develop a process, compound or product, including conducting non-clinical and clinical research and development activities. When used as a noun, “Development” means any and all activities involved in Developing.

“Effective Date” has the meaning set forth in the preamble to the Agreement.

“Existing Company Trial” means the Company’s currently ongoing multi-dose, 28 day study in healthy volunteers.

“FD&C Act” means the United States Federal Food, Drug, and Cosmetic Act, as amended, and the rules and regulations promulgated thereunder.

“FDA” means the United States Food and Drug Administration or any successor agency thereto.

“Field” means the treatment, prevention and diagnosis of all diseases and disorders.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-4

EXECUTION VERSION

“First Commercial Sale” means, with respect to any Licensed Product and with respect to any country of the Territory, the first sale of such Licensed Product by Pfizer or an Affiliate or Sublicensee of Pfizer to a Third Party in such country after such Licensed Product has been granted Regulatory Approval by the appropriate Regulatory Authority(ies) for such country.

“FSMA” means Families of Spinal Muscular Atrophy.

“FSMA-Company Agreement” means the Exclusive License Agreement, between Company and FSMA, dated October 22, 2009.

“GAAP” means United States generally accepted accounting principles, consistently applied.

“Generic Product” means any pharmaceutical product that [***].

“Governmental Authority” means any court, agency, department, authority or other instrumentality of any national, state, county, city or other political subdivision.

“IND” means an Investigational New Drug Application submitted under the FD&C Act, or an analogous application or submission with any analogous agency or Regulatory Authority outside of the United States for the purposes of obtaining permission to conduct Clinical Trials.

“Inventory” means the entire inventory of clinical and pre-clinical research-grade RG 3039, including the inventory set forth on Schedule A-1.

“Know-How” means proprietary and non-public ideas, concepts, discoveries, inventions developments and trade secrets (whether or not protectable under state, federal, or foreign patent, trade secret, trademark, copyright or similar laws), including development data, information, process, method, technique, material (including any chemical or biological material), technology or result, and any physical embodiments of any of the foregoing.

“Law” means any law, statute, rule, regulation, order, judgment or ordinance of any Governmental Authority.

“Licensed Product” means any product incorporating a Compound as an active ingredient (alone or with one or more other active ingredients), (i) a composition, the development, manufacture, use, sale or offer for sale of which, is Covered by a Valid Claim at any time during the Term in the country in which such product is developed, manufactured, used, sold or offered for sale, or (ii) that incorporates or relies upon the use of Company Know-How.

“Manufacture” or “Manufacturing” means to make, produce, manufacture, process, fill, finish, package, label, perform quality assurance testing, release, ship or store a compound or product or any component thereof. When used as a noun, “Manufacture” or “Manufacturing” means any and all activities involved in Manufacturing a compound or product or any component thereof.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-5

EXECUTION VERSION

“Milestone Event” means each milestone event listed in the table that appears in Section 3.2.1.

“Milestone Payment” means each milestone payment listed in the table that appears in Section 3.2.1.

“NDA” means a New Drug Application, as described in the FDA regulations, 21 CFR § 314.50, including all amendments and supplements to the application.

“Net Sales” means: (a) with respect to a Licensed Product that is not a Combination Product, gross receipts from sales by Pfizer and its Affiliates and Sublicensees of such Licensed Product to Third Parties in the Territory, less in each case [***]; and (b) with respect to a Licensed Product that is a Combination Product, [***].

“Patent Rights” means any and all (a) issued patents, (b) pending patent applications, including all provisional applications, substitutions, continuations, continuations-in-part, divisions and renewals, and all patents granted thereon, (c) patents-of-addition, reissues, reexaminations and extensions or restorations by existing or future extension or restoration mechanisms, including patent term adjustments, patent term extensions, supplementary protection certificates or the equivalent thereof, (d) inventor’s certificates, (e) other forms of government-issued rights substantially similar to any of the foregoing and (f) United States and foreign counterparts of any of the foregoing.

“Person” means an individual, sole proprietorship, partnership, limited partnership, limited liability partnership, corporation, limited liability company, business trust, joint stock company, trust, incorporated association, joint venture or similar entity or organization, including a government or political subdivision or department or agency of a government.

“Pfizer Quarter” means each of the four (4) thirteen (13) week periods (a) with respect to the United States, commencing on January 1 of any Pfizer Year and (b) with respect to any country in the Territory other than the United States, commencing on December 1 of any Pfizer Year.

“Pfizer Year” means the twelve month fiscal periods observed by Pfizer (a) commencing on January 1 with respect to the United States and (b) commencing on December 1 with respect to any country in the Territory other than the United States.

“Phase I Clinical Trial” means a Clinical Trial that will be the first test in SMA patients and will determine safety, metabolism and pharmacokinetics properties and clinical pharmacology of such product in patients that is generally consistent with 21CFR§ 312.21(a), as amended (or its successor regulations).

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-6

EXECUTION VERSION

“Phase Ib Clinical Trial” means a Clinical Trial, the principal purpose of which is to make a preliminary determination as to whether a pharmaceutical product is safe for it intended use and to obtain sufficient information about such product’s efficacy, in a manner that is generally consistent with 21 CFR § 312.21(b), as amended (or its successor regulation), to permit the design of further Clinical Trials.

“Phase IIb/III Clinical Trial” means a pivotal Clinical Trial (other than a Biomarker Trial) in human patients with a defined dose or a set of defined doses of a Licensed Product designed to ascertain efficacy and safety of such Licensed Product, in a manner that is generally consistent with 21 CFR § 312.21(c), as amended (or its successor regulation), for the purpose of enabling the preparation and submission of an NDA.

“Proof of Concept Phase Ib Trial” means a Clinical Trial which [***].

“Proof of Mechanism PhI Trial (POM)” means a Clinical Trial that [***].

“Price Approval” means, in any country where a Governmental Authority authorizes reimbursement for, or approves or determines pricing for, pharmaceutical products, receipt (or, if required to make such authorization, approval or determination effective, publication) of such reimbursement authorization or pricing approval or determination (as the case may be).

“Program Materials” means all (a) clinical samples, including human sera drawn from clinical trial subjects, collected in connection with the Development of the Compounds and/or Licensed Products, (b) all pre-clinical samples or biological materials collected or obtained specifically for use with the Development of the Compounds and/or Licensed Products, (c) laboratory reagents or supplies collected or obtained specifically for use with the Development of the Compounds and/or Licensed Products, and (d) any other biological, chemical or other materials, compositions of matter, articles of manufacture and assays used by or on behalf of Company (or its Affiliates) in connection with the Development of the Compounds and/or Licensed Products, in each such category to the extent Controlled by Company (or its Affiliates), including materials described on Schedule 4.3.2.

“Program Records” means all books, documents, data, regulatory files, correspondence, research, laboratory notebooks, manufacturing records, complaint records, study protocols, investigator brochures, adverse event information, and all other records and information (in paper, electronic or other form) relating to the Compounds and/or Licensed Products, including all data relating to or arising from the Development of Compounds and/or Licensed Products; provided, however, that: (a) Company may retain: (i) a copy of any such books, documents and records to the extent required by Law or necessary for tax, accounting or pending litigation purposes, including original copies to the extent required by Law and (ii) a copy of any such books, documents and records to the extent such books and records do not relate exclusively to Compounds or Licensed Products and are reasonably necessary for Company in connection with its other business activities; which copies retained under subsection (i) and (ii) shall be defined

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-7

EXECUTION VERSION

as “Retained Information” and deemed to be Pfizer Confidential Information subject to Company’s right to use such books and record solely for the aforementioned purposes; (b) any books, documents, correspondence and records of Company that Company reasonably determines, upon the advice of counsel, are attorney work product, attorney-client communications or other items protected by privilege immediately prior to the Effective Date shall be excluded from this definition of “Program Records” and shall be retained by Company; and (c) Company shall be entitled to redact from any Program Records any information that was not used in the Development of, and does not otherwise relate to, any Compounds and/or Licensed Products.

“Regulatory Approval” means all technical, medical and scientific licenses, registrations, authorizations and approvals (including approvals of NDAs, supplements and amendments, pre- and post- approvals, pricing and third party reimbursement approvals, and labeling approvals) of any Regulatory Authority, necessary for the research, use, Development, Manufacture, and Commercialization of a pharmaceutical product in a regulatory jurisdiction. For the sake of clarity, Regulatory Approval shall not be achieved for a Licensed Product in a country until all applicable Price Approvals and other Third Party reimbursement approvals have also been obtained by Pfizer or its designee for such Licensed Product in such country.

“Regulatory Authority” means, with respect to a country in the Territory, any national (e.g., the FDA), supra-national (e.g., the European Commission, the Council of the European Union, or the European Medicines Agency), regional, state or local regulatory agency, department, bureau, commission, council or other Governmental Authority involved in the granting of a Regulatory Approval or, to the extent required in such country, Price Approval, for pharmaceutical products in such country.

“Representatives” means (a) with respect to Pfizer, Pfizer, its Affiliates, its Sublicensees and each of their respective officers, directors, employees, consultants, contractors and agents and (b) with respect to Company, Company, its Affiliates and each of their respective officers, directors, employees, consultants, contractors and agents.

“Residual Knowledge” means knowledge, techniques, experience and Know-How that (a) are, or are based on any Confidential Information Controlled by the Disclosing Party and (b) are retained in the unaided memory of any authorized Representative of the Receiving Party after having access to such Confidential Information. In no event, however, will Residual Knowledge include any knowledge, techniques, experience and Know-How to the extent (at any time, for such time) within the scope of any issued, valid and enforceable patent claim Controlled by the Disclosing Party.

“Royalty Term” means on a Licensed Product-by-Licensed Product and country-by-country basis, the period from First Commercial Sale of a Licensed Product in such country until the later of (a) the time during which Manufacture, use or sale of such Licensed Product would no longer by Covered by a Valid Claim or (b) [***] years from the First Commercial Sale of the first Licensed Product in such country.

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-8

EXECUTION VERSION

“SMA” or “Spinal Muscular Atrophy” means a disease cause by decreased expression of the survival of motor neuron protein.

“SMA Compound/Product” means any compound or product [***].

“Sublicense” means a sublicense granted pursuant to a Sublicense Agreement.

“Sublicense Agreement” means an agreement pursuant to which any Third Party is granted a sublicense of intellectual property rights.

“Sublicensee” means any Person (other than an Affiliate) to whom Pfizer grants or has granted, directly or indirectly, a sublicense of rights licensed by Company to Pfizer under this Agreement.

“Territory” means all countries of the world.

“Third Party” means any Person other than Pfizer, Company or their respective Affiliates.

“Trademark” means any trademark, trade name, service mark, service name, brand, domain name, trade dress, logo, slogan or other indicia of origin or ownership, including the goodwill and activities associated with each of the foregoing.

“Trigger Date” has the meaning provided in the FSMA-Company Agreement.

“Valid Claim” means a claim in an issued and unexpired patent included in the Company Patent Rights, and that (a) has not been permanently revoked or held unenforceable or invalid by a decision of a court or governmental agency of competent jurisdiction, which decision is unappealable or unappealed within the time allowed for appeal, or (b) has not been abandoned, disclaimed, denied or admitted to be invalid or unenforceable through reissue or disclaimer or otherwise.

“[***]” means [***].

“[***]-FSMA Research Alliance” means, [***], by and between [***] and FSMA, [***], by and between [***] and FSMA, [***].

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-9

EXECUTION VERSION

The following terms are defined in the section of this Agreement listed opposite each term:

Defined Term	Section in Agreement
Additional Third Party License		3.3.3(f)
Agreement		Preamble
COMPANY		Preamble
COMPANY Indemnified Party		9.2
Debtor		8.6.1
Diligence Issue		4.5.4
Disclosed Third Party Agreement		7.3.10
Disclosing Party		6.1
Indemnified Party		9.4.1
Indemnifying Party		9.4.1
Liability		9.2
Litigation Conditions		9.4.2
Non-Disclosing Party		6.5.2
Notice of Dispute		10.10.1
Parties		Preamble
Party		Preamble
Pfizer		Preamble
Pfizer Indemnified Party		9.3
Receiving Party		6.1
Review Period		6.5.2
Selected Warning Notices		7.3.18
Term		8.1
Third Party Claim		9.4.1
VAT		3.4.3

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-10

EXECUTION VERSION

Exhibit B

Company Patent Rights Existing as of the Effective Date

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-11

EXECUTION VERSION

Exhibit C

Compounds Existing as of the Effective Date

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-12

EXECUTION VERSION

Schedule 4.3.1

Key Provisions for the Transition Services Agreement

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-13

EXECUTION VERSION

CORE TECHNOLOGIES FOR THE SMA/DCPS PROGRAM TRANSFER

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-14

EXECUTION VERSION

Schedule 4.3.2

Activities in Relation to Existing Clinical Trial

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-15

EXECUTION VERSION

Schedule 6.5.1

Company Press Release

Repligen Announces Licensing Agreement with Pfizer

for Spinal Muscular Atrophy Program

WALTHAM, MA – January 03, 2013 – Repligen Corporation (NASDAQ:RGEN) announced today that it has entered into an exclusive worldwide licensing agreement with Pfizer Inc. to advance Repligen’s spinal muscular atrophy (SMA) program, originally in-licensed from Families of SMA (FSMA). The SMA program includes RG3039, a small molecule drug candidate in clinical development for SMA, as well as backup compounds and enabling technologies. Under the terms of the agreement, Repligen is entitled to receive up to $70 million from Pfizer, commencing with an upfront payment of $5 million and total potential future milestone payments of up to $65 million as well as royalties on any future sales of SMA compounds developed under the agreement. SMA is an orphan neurodegenerative genetic disease that presents early in life.

“This agreement is consistent with the strategic decision we announced in August 2012 to focus Repligen’s internal efforts on the growth of our bioprocessing business, while seeking external partners for our therapeutic development programs,” said Walter C. Herlihy, Ph.D., President and Chief Executive Officer of Repligen. “We believe this collaboration with Pfizer, a leading pharmaceutical company with specialized efforts in orphan and genetic diseases, has the potential to accelerate the development of therapies for SMA.”

“There is a critical need to expedite potential treatment solutions for rare diseases such as spinal muscular atrophy, where patients have such limited options,” said Jose Carlos Gutierrez-Ramos, Senior Vice President, Pfizer BioTherapeutics R&D. “This partnership will combine our expert capabilities in advancing molecules for genetic diseases with Repligen’s leading SMA program.”

Under the terms of the agreement, Repligen is responsible for completing the first two cohorts of an active Phase 1 trial evaluating RG3039 in healthy volunteers, which it anticipates will occur during the first quarter of 2013. Repligen will also provide certain technology transfer services to Pfizer who will then assume full responsibility for the SMA program moving forward, including the conduct of any registration trials necessary for product approval. Repligen has previously received U.S. Orphan Drug and Fast Track designations for RG3039 for the treatment of SMA, as well as Orphan Medicinal Product designation in the EU.

“This licensing deal demonstrates the innovative collaborations that Families of SMA has successfully implemented between non-profit, biotech and big pharma,” stated Jill Jarecki, Ph.D., Research Director for Families of SMA. “These partnerships are critical for the development of new treatments for an orphan disease such as SMA. We are extremely pleased to see Pfizer taking the lead on the development and commercialization of the SMA program, following Repligen’s development work and FSMA’s original investment.”

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-16

EXECUTION VERSION

Families of SMA, a patient organization dedicated to funding research to advance therapies for SMA, funded and directed the preclinical development of RG3039 with an investment of more than $13 million. This was the first drug discovery program ever conducted specifically for SMA. Repligen’s research and clinical efforts, including the current Phase 1b trial, have been partially supported by a $1.4 million grant from the Muscular Dystrophy Association.

About Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease in which a defect in the SMN1 (survival motor neuron) gene results in low levels of the protein SMN and leads to progressive damage to motor neurons. It is the leading cause of infant mortality and the second most common inherited neuromuscular disease, with symptoms that typically emerge before the age of two. SMA is characterized by progressive muscle weakness leading to severe physical disability and often, early loss of life due to respiratory insufficiency.

About Families of SMA

Families of SMA is the world’s leader focused on funding SMA research to develop a treatment and cure for the disease. The successful results and progress that the organization has delivered, from basic research to drug discovery to clinical trials, provide real hope for families and patients impacted by the disease. The charity has invested over $55 million in research and has been involved in funding half of all the ongoing novel drug programs for SMA. Families of SMA is a nonprofit 501(c)3 organization, with 31 Chapters and 90,000 members and supporters throughout the United States. The organization’s work has produced major discoveries, including identification of the underlying cause and a back-up gene for the disease, which provides a clearly defined target for disease altering therapies. The organization is also dedicated to supporting SMA families through networking, information and services and to improving care for all SMA patients. For more information: www.curesma.org.

About the Muscular Dystrophy Association

The Muscular Dystrophy Association (MDA) is the leading nonprofit health agency dedicated to finding treatments and cures for more than 40 neuromuscular diseases, including SMA, by funding worldwide research. MDA also funds comprehensive health care and support services, advocacy, information and education, and accessible summer camp for thousands of youngsters fighting progressive muscle diseases. To date, MDA has invested more than $41.6 million in SMA research, funding basic research and clinical trials of therapeutic strategies such as gene-based therapies, small-molecule development, and stem cells. MDA, along with other SMA patient advocacy groups, has been working with policymakers to explore the potential of expanding newborn screening panels to include SMA. For more information, visit mda.org and follow MDA on Facebook (facebook.com/MDAnational) and Twitter (@MDAnews).

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-17

EXECUTION VERSION

Repligen Corporation

Repligen Corporation is a life sciences company focused on the development, production and commercialization of high-value consumable products used in the process of manufacturing biological drugs. Our bioprocessing products are sold to major life sciences and biopharmaceutical companies worldwide. We are a leading manufacturer of Protein A, a critical reagent used during the production of monoclonal antibody therapeutics. We also supply several growth factor products used to increase cell culture productivity during fermentation. In addition, we have developed and market a series of chromatography products used in the purification of biologics, and sell test kits to ensure final product quality. Aside from our core bioprocessing business, we have a portfolio of clinical-stage partnering assets, including a pancreatic imaging agent in Phase 3 development and two central nervous system orphan drug candidates. Repligen’s corporate headquarters are located in Waltham, MA, USA; we have an additional manufacturing facility in Lund, Sweden. For more information, please visit our website at www.repligen.com.

This press release contains forward-looking statements, which are made pursuant to the safe harbor provisions of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. Investors are cautioned that statements in this press release which are not strictly historical statements, including, without limitation, express or implied statements regarding the potential utility of RG3039 for the treatment of SMA, the clinical success of RG3039 and its further clinical development and our receipt of any future payments under the terms of our agreement with Pfizer, Pfizer’s ability to terminate the license agreement for convenience, our strategic decision to focus on the growth of our bioprocessing business, the future demand for our bioprocessing, growth factor and chromatography products, plans and objectives for future operations, our ability to successfully negotiate and consummate partnering transactions for our clinical stage assets, specifically RG1068, RG3039 and RG2833, plans and objectives for product development and acquisitions , plans and objectives for regulatory approval, product development, our market share and product sales and other statements identified by words like “believe,” “expect,” “may,” “will,” “should,” “seek,” or “could” and similar expressions, constitute forward-looking statements. Such forward-looking statements are subject to a number of risks and uncertainties that could cause actual results to differ materially from those anticipated, including, without limitation, risks associated with: the success of our clinical trials, including our Phase 1b clinical trial of RG3039 in patients with SMA; our ability to successfully grow our bioprocessing business, including as a result of acquisition, commercialization or partnership opportunities; our ability to successfully negotiate and consummate development and commercialization partnerships for our portfolio of clinical-stage assets on acceptable terms, if at all; our ability to develop and commercialize products and the market acceptance of our products; reduced demand for our products that adversely impacts our future revenues, cash flows, results of operations and financial condition; the ability to obtain, and the timing and receipt of, FDA approval for our NDA for RG3039; our ability to obtain other required regulatory approvals; the success of current and future collaborative or supply relationships, including our agreement with Pfizer; our ability to compete with larger,

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-18

EXECUTION VERSION

better financed bioprocessing, pharmaceutical and biotechnology companies; new approaches to the treatment of our targeted diseases; our compliance with all Food and Drug Administration and EMEA regulations; our ability to obtain, maintain and protect intellectual property rights for our products; the risk of litigation regarding our intellectual property rights; our limited sales capabilities; our volatile stock price; and other risks detailed in Repligen’s Annual Report on Form 10-K on file with the Securities and Exchange Commission and the other reports that Repligen periodically files with the Securities and Exchange Commission. Actual results may differ materially from those Repligen contemplated by these forward-looking statements. These forward looking statements reflect management’s current views and Repligen does not undertake to update any of these forward-looking statements to reflect a change in its views or events or circumstances that occur after the date hereof except as required by law.

Repligen Contact:

Sondra S. Newman

Director Investor Relations

snewman@repligen.com

(781) 419-1881

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-19

EXECUTION VERSION

Schedule 7.3.1

Intellectual Property Exceptions re: Ownership

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-20

EXECUTION VERSION

Schedule 7.3.8

Intellectual Property Exceptions re: Know-How

[***]

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-21

EXECUTION VERSION

Schedule 7.3.10

Disclosed Third Party Agreements

[***].

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-22

EXECUTION VERSION

Schedule A-1

Inventory

[***].

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH “[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934.

Exhibit A-23

EX-21.1

Exhibit 21.1

SUBSIDIARIES OF THE REGISTRANT

Repligen Europe Limited

Repligen Sweden AB

EX-23.1

Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We consent to the incorporation by reference in the following Registration Statements:

(1) Registration Statements (Form S-8 Nos. 333-157168, 333-89140 and 33-62796) pertaining to the Second Amended and Restated 2001 Repligen Corporation Stock Plan, the 2001 Repligen Corporation Stock Option Plan, and the 1992 Repligen Corporation Stock Plan

(2) Registration Statements (Form S-3 Nos. 333-106109, 333-30383, 333-57951, 333-76005, 333-79611, 333-95641, 333-31728, 333-35056 and 333-36280) of Repligen Corporation

of our reports dated March 15, 2013 with respect to the consolidated financial statements of Repligen Corporation and the effectiveness of internal control over financial reporting of Repligen Corporation, included in this Annual Report (Form 10-K) of Repligen Corporation for the year ended December 31, 2012.

/s/ Ernst & Young LLP

Boston, Massachusetts

March 15, 2013

EX-31.1

Exhibit 31.1

CERTIFICATION

I, Walter Herlihy, certify that:

1. I have reviewed this Annual Report on Form 10-K of Repligen Corporation;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report ) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: March 15, 2013

/S/    WALTER C. HERLIHY

Walter C. Herlihy

Chief Executive Officer and President

(Principal executive officer)

EX-31.2

Exhibit 31.2

CERTIFICATION

I, Jonathan Lieber, certify that:

1. I have reviewed this Annual Report on Form 10-K of Repligen Corporation;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report ) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: March 15, 2013

/S/    JONATHAN I. LIEBER

Jonathan I. Lieber

Chief Financial Officer

(Principal financial officer)

EX-32.1

Exhibit 32.1

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Annual Report of Repligen Corporation (the “Company”) on Form 10-K for the period ending December 31, 2012 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), the undersigned officers of the Company hereby certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, to my knowledge, that:

(1) The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: March 15, 2013	By:	/S/    WALTER C. HERLIHY
		Walter C. Herlihy
		Chief Executive Officer and President
		(Principal executive officer)
Date: March 15, 2013	By:	/S/    JONATHAN I. LIEBER
		Jonathan I. Lieber
		Chief Financial Officer
		(Principal financial officer)

XML

Percentage of Revenue from Significant Customers (Detail)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Orencia Royalties from Bristol
Revenue, Major Customer [Line Items]
Revenues, percentage by customer	37.00%	37.00%	24.00%	38.00%
Bioprocessing Customer A
Revenue, Major Customer [Line Items]
Revenues, percentage by customer	44.00%	45.00%	42.00%	42.00%

XML

Obligations Under Non Cancelable Operating Leases (Detail) (USD $)	Dec. 31, 2012
Schedule of Operating Leases [Line Items]
December 31, 2013	$ 2,222,000
December 31, 2014	2,222,000
December 31, 2015	2,222,000
December 31, 2016	2,222,000
December 31, 2017	1,655,000
Thereafter	5,611,000
Minimum lease payments	$ 16,154,000

XML

Stockholders' Equity - Additional Information (Detail) (USD $)	1 Months Ended	9 Months Ended		12 Months Ended
	Apr. 30, 2007	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2012	Mar. 31, 2011
Stockholders Equity Note Disclosure [Line Items]
Common stock, shares reserved				3,893,210
Common stock, shares purchased through issuance of warrants	150,000
Common stock, shares purchased through issuance of warrants per share	$ 0.01
Warrant term	7 years
Stock-based compensation expense		$ 730,136	$ 748,235	$ 1,024,152		$ 1,003,266
Stock options outstanding		2,823,400	2,566,450	2,315,090
Closing price of the common stock				$ 6.28
Aggregate intrinsic value of stock options exercised		8,000	43,000	1,384,000	76,000
Weighted average grant date fair value of share-based awards granted		$ 1.89	$ 1.95	$ 3.62		$ 2.11
Total fair value of stock options vested		804,000	817,000	931,000		993,000
Total unrecognized compensation cost				$ 1,605,995
Unrecognized compensation cost, weighted average remaining requisite service period				2 years 9 months 4 days
Number of unvested options				739,009
2012 Plan
Stockholders Equity Note Disclosure [Line Items]
Number of shares available for future grant				1,578,120
Employee Stock Option | Minimum
Stockholders Equity Note Disclosure [Line Items]
Incentive options, vesting period				4 years
Incentive options, vesting on the first anniversary of the date of grant				20.00%
Employee Stock Option | Maximum
Stockholders Equity Note Disclosure [Line Items]
Incentive options, vesting period				5 years
Incentive options, vesting on the first anniversary of the date of grant				25.00%
Incentive options, term				10 years
Non-Employee Directors and Consultants
Stockholders Equity Note Disclosure [Line Items]
Incentive options, vesting period				1 year
Unvested Options
Stockholders Equity Note Disclosure [Line Items]
Incentive options, vesting period				5 years

XML

Prepaid Expenses and Other Current Assets (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Prepaid Expenses And Other Current Assets [Line Items]
Equipment maintenance and services	$ 747,273	$ 424,328
Prepaid insurance	365,167	251,418
Interest receivable	140,363	106,695
Clinical and research expenses	15,354	13,714
Other	36,730	82,304
Total	$ 1,304,887	$ 878,459

XML

Consolidated Deferred Tax Assets or Liabilities (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Deferred tax assets:
Temporary timing differences	$ 4,152,000	$ 4,277,000
Net operating loss carryforwards	15,041,000	20,065,000
Tax business credits carryforwards	2,160,000	4,166,000
Total deferred tax assets	21,353,000	28,508,000
Valuation allowance	(18,307,000)	(28,476,000)
Net deferred tax assets	3,046,000	32,000
Deferred tax liabilities:
Goodwill	(72,000)	(48,000)
Acquired intangibles		(89,000)
Net deferred tax assets (liabilities)	$ 2,974,000	$ (105,000)

XML

Schedule of Inventories (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Schedule of Inventory [Line Items]
Raw Materials	$ 4,064,317	$ 3,563,395
Work-in-process	4,112,478	5,936,578
Finished products	2,966,900	3,863,100
Total	$ 11,143,695	$ 13,363,073

XML

Employee Benefit Plans - Additional Information (Detail) (USD $)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Minimum
Deferred Compensation Arrangement with Individual, Postretirement Benefits [Line Items]
Defined contribution plan, eligible age of employees			21
Defined Contribution 401 K Plan
Deferred Compensation Arrangement with Individual, Postretirement Benefits [Line Items]
Defined contribution plan, company contribution	$ 102,000	$ 108,000	$ 103,000	$ 108,000
Pension Plans, Defined Benefit | Sweden
Deferred Compensation Arrangement with Individual, Postretirement Benefits [Line Items]
Defined contribution plan, company contribution	$ 10,000		$ 532,000

XML

Accrued Liabilities (Tables)

12 Months Ended

Dec. 31, 2012

Schedule of Accrued Liabilities

Accrued liabilities consist of the following:

	December 31, 2012		December 31, 2011
Employee compensation	$	3,634,839	$	2,741,738
Royalty and license fees		1,459,680		499,776
Contingent consideration		1,376,877		35,000
Unearned revenue		599,120		469,046
Professional fees		418,800		871,086
VAT liabilities		98,162		566,542
Research and development		18,300		142,695
Other accrued expenses		692,212		715,155
Total	$	8,297,990	$	6,041,038

XML

Estimated Weighted Average Assumptions (Detail)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2011	Mar. 31, 2011
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (years)	6 years 6 months	6 years 6 months	6 years 6 months	6 years 6 months
Volatility, minimum	53.09%	57.58%	49.76%	55.94%
Volatility, maximum	55.76%	63.60%	53.54%	63.60%
Risk-free interest rate, minimum	1.25%	1.81%	0.89%	1.81%
Risk-free interest rate, maximum	2.38%	2.62%	1.06%	2.83%
Expected dividend yield

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Income from Operations Before Income Taxes (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Dec. 31, 2011	Mar. 31, 2011
Schedule of Income Before Income Tax [Line Items]
Domestic											$ 11,175,638	$ (1,845,024)	$ (43,509)
Foreign											95,768	248,143
Income (loss) before income taxes	$ 6,418,000	$ 1,790,000	$ 1,778,000	$ 1,285,000	$ (2,146,000)	$ 605,000	$ (55,000)	$ (2,030,000)	$ (1,596,881)	$ 1,987,178	$ 11,271,406	$ (1,596,881)	$ (43,509)

XML

Total Assets by Geographic Area (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Segment Reporting, Asset Reconciling Item [Line Items]
Asset	$ 97,010,163	$ 76,056,814
United States
Segment Reporting, Asset Reconciling Item [Line Items]
Asset	58,356,697	44,223,080
Sweden
Segment Reporting, Asset Reconciling Item [Line Items]
Asset	$ 38,653,466	$ 31,833,734

XML

Summary of Information Regarding Option Activity (Parenthetical) (Detail)	Dec. 31, 2012
Awards Granted to Non-Executive Level Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated forfeiture rates	8.00%
Awards Granted to Executive Level Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated forfeiture rates	3.00%

XML

Total Consideration Transferred (Detail) (Novozymes Biopharma Sweden Ab, USD $)	Dec. 20, 2011
Novozymes Biopharma Sweden Ab
Business Acquisition [Line Items]
Cash consideration	$ 26,445,000
Estimated fair value of contingent consideration	1,611,000
Total consideration transferred	$ 28,056,000

XML

Reconciliation of Federal Statutory Rate to Effective Income Tax Rate (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Dec. 31, 2011	Mar. 31, 2011
Income Tax Rate Reconciliation [Line Items]
Income (loss) before income taxes	$ 6,418,000	$ 1,790,000	$ 1,778,000	$ 1,285,000	$ (2,146,000)	$ 605,000	$ (55,000)	$ (2,030,000)	$ (1,596,881)	$ 1,987,178	$ 11,271,406	$ (1,596,881)	$ (43,509)
Expected tax (recovery) at statutory rate									(542,939)		3,944,996		(14,793)
Adjustments due to:
Difference between U.S. and foreign tax									(19,287)		(8,332)
State income and franchise taxes									52,905		357,866		96,141
Business tax credits									(68,926)		(67,276)		(66,126)
Transaction costs									240,842
Gain on bargain purchase									(112,427)		(82,422)
Permanent differences									218,989		242,629		250,483
Change in valuation allowance									246,587		(7,272,092)		(265,706)
Provision (benefit) for income taxes									$ 15,744		$ (2,884,631)
Expected tax (recovery) at statutory rate									(34.00%)		35.00%		(34.00%)
Adjustments due to:
Difference between U.S. and foreign tax									(1.20%)		(0.10%)		0.00%
State income and franchise taxes									3.30%		3.20%		221.00%
Business tax credits									(4.30%)		(0.60%)		(152.00%)
Transaction costs									15.10%		0.00%		0.00%
Gain on bargain purchase									(7.00%)		(0.70%)		0.00%
Permanent differences									13.70%		2.10%		575.70%
Change in valuation allowance									15.40%		(64.50%)		(610.70%)
Provision (benefit) for income taxes									1.00%		(25.60%)		0.00%

XML

Income Taxes

12 Months Ended

Dec. 31, 2012

Income Taxes

3. Income Taxes

Income tax data for the year ended December 31, 2012, the nine months ended December 31, 2011 and the year ended March 31, 2011:

	December 31, 2012			December 31, 2011			March 31, 2011
The components of income from operations before income taxes are as follows:
Domestic	$	11,175,638		$	(1,845,024	)	$	(43,509	)
Foreign		95,768			248,143			—
Total	$	11,271,406		$	(1,596,881	)	$	(43,509	)
The current and deferred components of the provision for income taxes on operations are as follows:
Current	$	312,630		$	—		$	—
Deferred		(3,197,261	)		15,774			—
Total	$	(2,884,631	)	$	15,774		$	—
The jurisdictional components of the provision for income taxes on operations are as follows:
Federal	$	(2,915,673	)	$	48,000		$	—
State		115,307			—			—
Foreign		(84,265	)		(32,226	)		—
Total	$	(2,884,631	)	$	15,774		$	—

At December 31, 2012, the Company had net operating loss carryforwards of approximately $44,678,000 and business tax credits carryforwards of approximately $2,160,000 available to reduce future federal income taxes, if any. The U.S. federal net operating loss includes $441,000 related to excess tax deductions from share-based payments, the tax benefit of which will be recognized as an increase to additional paid in capital when the deduction reduces current taxes payable. The net operating loss and business tax credits carryforwards will continue to expire at various dates through December 2032. The net operating loss and business tax credit carryforwards are subject to review and possible adjustment by the Internal Revenue Service and may be limited in the event of certain changes in the ownership interest of significant stockholders.

The Company’s consolidated deferred tax assets (liabilities) consist of the following:

	December 31, 2012			December 31, 2011
Deferred tax assets:
Temporary timing differences	$	4,152,000		$	4,277,000
Net operating loss carryforwards		15,041,000			20,065,000
Tax business credits carryforwards		2,160,000			4,166,000
Total deferred tax assets		21,353,000			28,508,000
Valuation allowance		(18,307,000	)		(28,476,000	)
Net deferred tax assets	$	3,046,000		$	32,000
Deferred tax liabilities:
Goodwill	$	(72,000	)	$	(48,000	)
Acquired intangibles		—			(89,000	)
Net deferred tax assets (liabilities)	$	2,974,000		$	(105,000	)

The net change in the total valuation allowance was a decrease of $10,169,000 in the year ended December 31, 2012. The valuation allowance increased by $73,000 for the nine months ended December 31, 2011 and increased by $2,227,000 for the year ended March 31, 2011. As of September 30, 2012, the Company’s U.S. net operating losses (“NOL’s”) and other deferred tax assets were fully offset by a valuation allowance primarily because the Company was in a cumulative loss position and did not have sufficient history of income to conclude that it was more likely than not that the Company would be able to realize the tax benefits of those deferred tax assets. In the fourth quarter of 2012, the Company entered into a three-year cumulative pre-tax income position and concluded that it was more likely than not that it will generate sufficient taxable income in 2013 based on its 2013 projections to realize the tax benefit of a portion of its deferred tax assets. Thus, the Company reversed $3,021,000 of the deferred tax asset valuation allowance in the U.S in the fourth quarter of 2012. The amount is recorded as a benefit for income taxes in the Company’s consolidated statements of operations and comprehensive income (loss). The Company concluded that realization of deferred tax assets beyond December 31, 2013 is not more likely than not as a result of the fact that the Company will not receive royalty payments from Bristol on U.S. net sales of Orencia after December 31, 2013, and as such, the Company continues to maintain a valuation allowance against those deferred tax assets estimated to reverse beyond 2013.

The reconciliation of the federal statutory rate to the effective income tax rate for the year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011 is as follows:

	Period Ended,
	December 31, 2012					December 31, 2011					March 31, 2011
Income (loss) before income taxes	$	11,271,406			%	$	(1,596,881	)		%	$	(43,509	)		%
Expected tax (recovery) at statutory rate		3,944,996		35.0	%		(542,939	)	(34.0	)%		(14,793	)	(34.0	)%
Adjustments due to:
Difference between U.S. and foreign tax		(8,332	)	(0.1	)%		(19,287	)	(1.2	)%		—		(0.0	)%
State income and franchise taxes		357,866		3.2	%		52,905		3.3	%		96,141		221.0	%
Business tax credits		(67,276	)	(0.6	)%		(68,926	)	(4.3	)%		(66,126	)	(152.0	)%
Transaction costs		—		0.0	%		240,842		15.1	%		—		0.0	%
Gain on bargain purchase		(82,422	)	(0.7	)%		(112,427	)	(7.0	)%		—		(0.0	)%
Permanent differences		242,629		2.1	%		218,989		13.7	%		250,483		575.7	%
Change in valuation allowance		(7,272,092	)	(64.5	)%		246,587		15.4	%		(265,706	)	(610.7	)%
Provision (benefit) for income taxes	$	(2,884,631	)	(25.6	)%	$	15,744		1.0	%	$	—		(0.0	)%

At December 31, 2012 and 2011 as well as March 31, 2011, the Company had no material unrecognized tax benefits.

The Company recognizes interest and penalties related to uncertain tax positions in income tax expense. No interest and penalties have been recognized by the Company to date.

The fiscal years ended March 31, 2007 through March 31, 2011 as well as the nine-month fiscal year ended December 31, 2011 and the year ended December 31, 2012 are subject to examination by the federal and state taxing authorities. Currently, a corporate excise tax audit is underway in the Commonwealth of Massachusetts for the fiscal years ended March 31, 2007 and 2008. To date, no assessments have been made and the Company continues to believe no reserve is required.

At December 31, 2012, the Company has not provided for U.S. income taxes or foreign withholding taxes on outside basis differences of foreign subsidiaries of approximately $477,000 as it is the Company’s current intention to permanently reinvest these earnings outside the U.S.

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Summary of allocation of fair value of assets acquired and liabilities assumed (Detail) (USD $)	3 Months Ended		9 Months Ended	12 Months Ended
	Mar. 31, 2012	Dec. 31, 2011	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2012 Novozymes Biopharma Sweden Ab	Dec. 20, 2011 Novozymes Biopharma Sweden Ab
Business Acquisition [Line Items]
Accounts receivable					$ 5,088,000
Inventory					10,497,000
Prepaid expenses					180,000
Fixed assets					9,089,000
Customer relationships and acquired technology					6,705,000
Deferred tax liability					(198,000)
Accounts payable and other liabilities assumed					(2,563,000)
Net assets acquired					28,798,000
Less total consideration transferred					(28,056,000)	(28,495,000)
Gain on bargain purchase	$ 314,000	$ 427,000	$ 427,478	$ 314,244	$ 742,000

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Current and Deferred Income Taxes (Detail) (USD $)	3 Months Ended					9 Months Ended	12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Income Taxes [Line Items]
Current							$ 312,630
Deferred							(3,197,261)	15,774
Total	$ (3,135,000)	$ (16,000)	$ 208,000	$ 59,000	$ 16,000	$ 15,744	$ (2,884,631)	$ 15,774

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Investments in Debt Securities (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 20,745,938	$ 24,850,448
Gross Unrealized Gain	15,479	11,032
Gross Unrealized Loss	(1,367)	(4,694)
Fair Value	20,760,050	24,856,786
Marketable securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	10,835,995	15,419,577
Gross Unrealized Gain	9,207	6,462
Gross Unrealized Loss	(7)	(4,603)
Fair Value	10,845,195	15,421,436
Marketable securities | U.S. Government and agency securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	2,000,897	8,373,355
Gross Unrealized Gain	353	3,126
Gross Unrealized Loss	(7)	(233)
Fair Value	2,001,243	8,376,248
Marketable securities | Corporate and other debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	8,835,098	7,046,222
Gross Unrealized Gain	8,854	3,336
Gross Unrealized Loss		(4,370)
Fair Value	8,843,952	7,045,188
Long-term marketable securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	9,909,943	9,430,871
Gross Unrealized Gain	6,272	4,570
Gross Unrealized Loss	(1,360)	(91)
Fair Value	9,914,855	9,435,350
Long-term marketable securities | U.S. Government and agency securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	5,198,264	8,399,428
Gross Unrealized Gain	2,747	2,223
Gross Unrealized Loss		(91)
Fair Value	5,201,011	8,401,560
Long-term marketable securities | Corporate and other debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	4,711,679	1,031,443
Gross Unrealized Gain	3,525	2,347
Gross Unrealized Loss	(1,360)
Fair Value	$ 4,713,844	$ 1,033,790

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Summary of Significant Accounting Policies - Additional Information (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended
	Dec. 31, 2012 Investment	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012 Segment Investment	Dec. 31, 2011	Mar. 31, 2011
Summary Of Significant Accounting Policies [Line Items]
Royalty revenue	$ 9,104,000	$ 3,981,000	$ 3,865,000	$ 3,482,000	$ 4,051,000	$ 2,889,000	$ 3,295,000	$ 2,756,000	$ 10,235,194	$ 9,573,770	$ 20,432,348		$ 12,329,627
Revenue from sponsored research and development projects under agreements with the National Institutes of Health											803,000
Revenue from sponsored research and development projects									1,466,000	1,102,000			1,346,000
Marketable securities, average remaining contractual maturity period					9 months 27 days				9 months 27 days			9 months 27 days
Number of debt securities in unrealized loss positions	7										7
Debt securities in unrealized loss positions, total unrealized loss	1,000										1,000
Debt securities in unrealized loss positions, total fair market value	2,667,000										2,667,000
Reserves for excess and obsolete inventory	154,000				149,000			50,000	149,000	50,000	154,000	149,000	50,000
Depreciation expense of property and equipment									1,117,000	1,141,000	2,492,000		1,496,000
Stock options, outstanding	2,315,090				2,823,400				2,823,400	2,566,450	2,315,090	2,823,400
Stock options, weighted average exercise price	$ 4.20				$ 4.05				$ 4.05	$ 4.08	$ 4.20	$ 4.05
Common stock excluded from calculation of diluted earnings per share									2,823,400	1,771,100	1,296,700		2,580,600
Number of operating segment											1
Amortization expense									158,000	134,000	1,017,000	179,000
Expected amortization expense in 2013	1,000,000										1,000,000
Expected amortization expense in 2014	1,000,000										1,000,000
Expected amortization expense in 2015	1,000,000										1,000,000
Expected amortization expense in 2016	1,000,000										1,000,000
Expected amortization expense in 2017	1,000,000										1,000,000
Expected dividend yield											0
Non-Executive Employees
Summary Of Significant Accounting Policies [Line Items]
Estimated annual forfeiture rates											8.00%
Awards Granted to Executive Level Employees
Summary Of Significant Accounting Policies [Line Items]
Estimated annual forfeiture rates											3.00%
Assets Held under Capital Leases
Summary Of Significant Accounting Policies [Line Items]
Depreciation expense of property and equipment										82,000			82,000
Minimum
Summary Of Significant Accounting Policies [Line Items]
Marketable securities, minimum original maturity term	90 days										90 days
Long-term marketable securities, minimum original maturity term	1 year										1 year
Bristol Myers Squibb Company
Summary Of Significant Accounting Policies [Line Items]
Royalty revenue									8,769,000		14,753,000		10,251,000
Qualifying Therapeutic Discovery Project Program
Summary Of Significant Accounting Policies [Line Items]
Revenue from sponsored research and development projects										$ 733,000			$ 733,000

XML

Schedule of Accrued Liabilities (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Schedule of Accrued Liabilities [Line Items]
Employee compensation	$ 3,634,839	$ 2,741,738
Royalty and license fees	1,459,680	499,776
Contingent consideration	1,376,877	35,000
Unearned revenue	599,120	469,046
Professional fees	418,800	871,086
VAT liabilities	98,162	566,542
Research and development	18,300	142,695
Other accrued expenses	692,212	715,155
Total	$ 8,297,990	$ 6,041,038

XML

Provision for Income Taxes by Jurisdiction (Detail) (USD $)	3 Months Ended					9 Months Ended	12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Income Taxes [Line Items]
Federal							$ (2,915,673)	$ 48,000
State							115,307
Foreign							(84,265)	(32,226)
Total	$ (3,135,000)	$ (16,000)	$ 208,000	$ 59,000	$ 16,000	$ 15,744	$ (2,884,631)	$ 15,774

XML

Contractual Maturities of Debt Securities (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Schedule of Available-for-sale Securities [Line Items]
Due in 1 year or less	$ 10,835,995
Due in 1 to 2 years	9,909,943
Amortized Cost	20,745,938	24,850,448
Due in 1 year or less	10,845,195
Due in 1 to 2 years	9,914,855
Fair Value	$ 20,760,050	$ 24,856,786

XML

Major Category of Assets Measured at Fair Value on Recurring Basis (Detail) (Fair Value, Measurements, Recurring, USD $)	Dec. 31, 2012
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	$ 29,551,078
Money Market Funds
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	7,891,062
U.S. Government and agency securities
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	8,102,220
Corporate and other debt securities
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	13,557,796
Quoted prices in active markets for identical assets (Level 1)
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	10,792,271
Quoted prices in active markets for identical assets (Level 1) | Money Market Funds
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	7,891,062
Quoted prices in active markets for identical assets (Level 1) | U.S. Government and agency securities
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	2,901,209
Significant other observable inputs (Level 2)
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	18,758,807
Significant other observable inputs (Level 2) | U.S. Government and agency securities
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	5,201,011
Significant other observable inputs (Level 2) | Corporate and other debt securities
Fair Value, Assets and Liabilities Measured on Recurring Basis [Line Items]
Assets	$ 13,557,796

XML

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2012

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States (“GAAP”) requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Consolidation

The consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Repligen Europe Limited and Repligen Sweden AB. All significant intercompany accounts and transactions have been eliminated in consolidation.

Foreign Currency

The Company translates the assets and liabilities of foreign subsidiaries at rates in effect at the end of the reporting period. Revenues and expenses are translated at average rates in effect during the reporting period. Translation adjustments are included in accumulated other comprehensive income.

Revenue Recognition

Product Sales

The Company generates product revenues from the sale of bioprocessing products to customers in the pharmaceutical and process chromatography industries. The Company recognizes revenue related to product sales upon delivery of the product to the customer as long as there is persuasive evidence of an arrangement, the sales price is fixed or determinable and collection of the related receivable is reasonably assured. Determination of whether these criteria have been met is based on management’s judgments primarily regarding the fixed nature of the fee charged for the product delivered and the collectability of those fees. The Company has a few longstanding customers who comprise the majority of revenue and have excellent payment histories and therefore the Company does not require collateral. The Company has had no significant write-offs of uncollectible invoices in the periods presented.

At the time of sale, the Company also evaluates the need to accrue for warranty and sales returns. The supply agreements the Company has with its customers and related purchase orders identify the terms and conditions of each sale and the price of the goods ordered. Due to the nature of the sales arrangements, inventory produced for sale is tested for quality specifications prior to shipment. Since the product is manufactured to order and in compliance with required specifications prior to shipment, the likelihood of sales return, warranty or other issues is largely diminished. Sales returns and warranty issues are infrequent and have had nominal impact on the Company’s consolidated financial statements historically.

Orencia Royalty

In April 2008, the Company settled its outstanding litigation with Bristol and began recognizing royalty revenue in fiscal year 2009 for Bristol’s net sales in the United States of Orencia^®, which is used in the treatment of rheumatoid arthritis. Pursuant to the settlement with Bristol (see Note 9), the Company recognized royalty revenue of $14,753,000 for the fiscal year ended December 31, 2012, $8,769,000 for the nine-month fiscal year ended December 31, 2011 and $10,251,000 for the fiscal year ended March 31, 2011. Revenue earned from Bristol royalties is recorded in the periods when it is earned based on royalty reports sent by Bristol to the Company. The Company has no continuing obligations to Bristol as a result of this settlement. The Company’s royalty agreement with Bristol provides that the Company will receive such royalty payments from Bristol through December 31, 2013.

Therapeutics Licensing Agreements

Activities under licensing agreements are evaluated in accordance with ASC 605-25 to determine if they represent a multiple element revenue arrangement. The Company identifies the deliverables included within the agreement and evaluates which deliverables represent separate units of accounting. The Company accounts for those components as separate units of accounting if the following two criteria are met:

• The delivered item or items have value to the customer on a stand-alone basis.

• If there is a general right of return relative to the delivered items, delivery or performance of the undelivered items is considered probable and within our control.

Factors considered in this determination include, among other things, whether any other vendors sell the items separately and if the licensee could use the delivered item for its intended purpose without the receipt of the remaining deliverables. If multiple deliverables included in an arrangement are separable into different units of accounting, the Company allocates the arrangement consideration to those units of accounting. The amount of allocable arrangement consideration is limited to amounts that are fixed or determinable. Arrangement consideration is allocated at the inception of the arrangement to the identified units of accounting based on their relative selling price. Revenue is recognized for each unit of accounting when the appropriate revenue recognition criteria are met.

Future milestone payments, if any, under a license agreement will be recognized under the provisions of ASC 605-28, which the Company adopted on January 1, 2011. The Company has elected to recognize a payment that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is substantive if:

• It can only be achieved based in whole or in part on either (1) the Company’s performance or (2) on the occurrence of a specific outcome resulting from the Company’s performance;

• There is substantive uncertainty at the date an arrangement is entered into that the event will be achieved; and

• It would result in additional payments being due to the entity.

The Company believes that the clinical milestone payments pursuant to the license agreement with Pfizer, Inc. (“Pfizer”), as described in Note 10, are substantive and thus will be recognized when achieved. The commercial milestone payments and royalty payments received under license agreements, if any, will be recognized as revenue when they are earned.

Research and Development Agreements

In the fiscal year ended December 31, 2012, the Company recognized $803,000 of revenue from sponsored research and development projects under agreements with the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, GoFar, and the Friedreich’s Ataxia Research Alliance.

For the nine-month fiscal year ended December 31, 2011, the Company recognized $1,466,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, Go Friedreich’s Ataxia Research (“GoFar”), and the Friedreich’s Ataxia Research Alliance. For the nine-month period ended December 31, 2010, the Company recognized $1,102,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. For the nine months ended December 31, 2010, the Company also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

In the fiscal year ended March 31, 2011, the Company recognized $1,346,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. During the year ended March 31, 2011, the Company also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

Research revenue is recognized when the expense has been incurred and services have been performed. Determination of which costs incurred qualify for reimbursement under the terms of the Company’s contractual agreements and the timing of when such costs were incurred involves the judgment of management. The Company’s calculations are based upon the agreed-upon terms as stated in the arrangements. However, should the estimated calculations change or be challenged by other parties to the agreements, research revenue may be adjusted in subsequent periods. The calculations have not historically changed or been challenged and the Company does not anticipate any subsequent change in its revenue related to sponsored research and development projects.

There have been no material changes to the Company’s initial estimates related to revenue recognition in any periods presented in the accompanying consolidated financial statements.

Risks and Uncertainties

The Company evaluates its operations periodically to determine if any risks and uncertainties exist that could impact its operations in the near term. The Company does not believe that there are any significant risks which have not already been disclosed in the consolidated financial statements. A loss of certain suppliers could temporarily disrupt operations, although alternate sources of supply exist for these items. The Company has mitigated these risks by working closely with key suppliers, identifying alternate sources and developing contingency plans.

Cash, Cash Equivalents and Marketable Securities

At December 31, 2012 and December 31, 2011, the Company’s investments included money market funds as well as short-term and long-term marketable securities. Marketable securities are investments with original maturities of greater than 90 days. Long-term marketable securities are securities with maturities of greater than one year. The average remaining contractual maturity of marketable securities at December 31, 2012 is approximately 9.9 months.

Investments in debt securities consisted of the following at December 31, 2012:

	December 31, 2012
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	2,000,897	$	353	$	(7	)	$	2,001,243
Corporate and other debt securities		8,835,098		8,854		—			8,843,952
		10,835,995		9,207		(7	)		10,845,195
Long-term marketable securities:
U.S. Government and agency securities		5,198,264		2,747		—			5,201,011
Corporate and other debt securities		4,711,679		3,525		(1,360	)		4,713,844
		9,909,943		6,272		(1,360	)		9,914,855
Total	$	20,745,938	$	15,479	$	(1,367	)	$	20,760,050

At December 31, 2012, the Company’s investments included seven debt securities in unrealized loss positions with a total unrealized loss of approximately $1,000 and a total fair market value of approximately $2,667,000. All investments with gross unrealized losses have been in unrealized loss positions for less than 12 months. The unrealized losses were caused primarily by current economic and market conditions. There was no change in the credit risk of the securities. The Company does not intend to sell any investments in an unrealized loss position and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases. There were no realized gains or losses on the investments for the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011 or the fiscal year ended March 31, 2011.

Investments in debt securities consisted of the following at December 31, 2011:

	December 31, 2011
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	8,373,355	$	3,126	$	(233	)	$	8,376,248
Corporate and other debt securities		7,046,222		3,336		(4,370	)		7,045,188
		15,419,577		6,462		(4,603	)		15,421,436
Long-term marketable securities:
U.S. Government and agency securities		8,399,428		2,223		(91	)		8,401,560
Corporate and other debt securities		1,031,443		2,347		—			1,033,790
		9,430,871		4,570		(91	)		9,435,350
Total	$	24,850,448	$	11,032	$	(4,694	)	$	24,856,786

The contractual maturities of debt securities at December 31, 2012 were as follows:

	Amortized Cost		Fair Value
Due in 1 year or less	$	10,835,995	$	10,845,195
Due in 1 to 2 years		9,909,943		9,914,855
	$	20,745,938	$	20,760,050

Fair Value Measurement

In determining the fair value of its assets and liabilities, the Company uses various valuation approaches. The Company employs a hierarchy for inputs used in measuring fair value that maximizes the use of observable inputs and minimizes the use of unobservable inputs by requiring that observable inputs be used when available. Observable inputs are inputs that market participants would use in pricing the asset or liability based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the asset or liability and are developed based on the best information available in the circumstances. The fair value hierarchy is broken down into three levels based on the source of inputs as follows:

Level 1	—	Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access.
Level 2	—	Valuations based on quoted prices for similar assets or liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active and models for which all significant inputs are observable, either directly or indirectly.
Level 3	—	Valuations based on inputs that are unobservable and significant to the overall fair value measurement.

The availability of observable inputs can vary among the various types of financial assets and liabilities. To the extent that the valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. In certain cases, the inputs used to measure fair value may fall into different levels of the fair value hierarchy. In such cases, for financial statement disclosure purposes, the level in the fair value hierarchy within which the fair value measurement is categorized is based on the lowest level input that is significant to the overall fair value measurement.

The Company’s fixed income investments are comprised of obligations of U.S. government agencies, corporate debt securities and other interest bearing securities. These investments have been initially valued at the transaction price and subsequently valued, at the end of each reporting period, utilizing third party pricing services or other market observable data. The pricing services utilize industry standard valuation models, including both income and market based approaches and observable market inputs to determine value. These observable market inputs include reportable trades, benchmark yields, credit spreads, broker/dealer quotes, bids, offers, current spot rates and other industry and economic events. The Company validates the prices provided by third party pricing services by reviewing their pricing methods and matrices, obtaining market values from other pricing sources, analyzing pricing data in certain instances and confirming that the relevant markets are active. After completing its validation procedures, the Company did not adjust or override any fair value measurements provided by the pricing services as of December 31, 2012.

The following fair value hierarchy table presents information about each major category of the Company’s assets measured at fair value on a recurring basis as of December 31, 2012:

	Fair value measurement at reporting date using:
	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Total
Assets:
Money market funds	$	7,891,062	$	—	$	—	$	7,891,062
U.S. Government and agency securities		2,901,209		5,201,011		—		8,102,220
Corporate and other debt securities		—		13,557,796		—		13,557,796
Total	$	10,792,271	$	18,758,807	$	—	$	29,551,078

The Company has no other assets or liabilities for which fair value measurement is either required or has been elected to be applied, other than the liabilities for contingent consideration recorded in connection with the Novozymes Acquisition and the acquisition of the assets of BioFlash Partners, LLC (“BioFlash”). The contingent consideration related to Novozymes is valued using management’s estimates of expected future milestone payments based upon a probability weighted analysis of amounts to be paid to Novozymes Denmark. The contingent consideration related to BioFlash is valued using management’s estimates of royalties to be paid to the former shareholders of BioFlash based on sales of the acquired assets. These valuations are Level 3 valuations as the primary inputs are unobservable. Changes in the fair value of contingent consideration in the year ended December 31, 2012 are primarily attributable to changes in the probability of the Company making certain contingent payments. The following table provides a roll forward of the fair value of the contingent consideration:

Balance at December 31, 2011	$	2,197,226
Additions		—
Payments		(35,000	)
Changes in fair value		736,850
Balance at December 31, 2012	$	2,899,076

There were no remeasurements to fair value during the year ended December 31, 2012 of financial assets and liabilities that are not measured at fair value on a recurring basis.

Inventories

Inventories relate to the Company’s bioprocessing business. The Company values inventory at cost or, if lower, fair market value, using the first-in, first-out method. The Company reviews its inventories at least quarterly and records a provision for excess and obsolete inventory based on its estimates of expected sales volume, production capacity and expiration dates of raw materials, work-in process and finished products. Expected sales volumes are determined based on supply forecasts provided by key customers for the next three to 12 months. The Company writes down inventory that has become obsolete, inventory that has a cost basis in excess of its expected net realizable value, and inventory in excess of expected requirements to cost of product revenue. Manufacturing of bioprocessing finished goods is done to order and tested for quality specifications prior to shipment. Reserves for excess and obsolete inventory were $154,000 and $149,000 as of December 31, 2012 and 2011, respectively. At both December 31, 2010 and March 31, 2011, reserves for excess and obsolete inventory were $50,000.

A change in the estimated timing or amount of demand for the Company’s products could result in additional provisions for excess inventory quantities on hand. Any significant unanticipated changes in demand or unexpected quality failures could have a significant impact on the value of inventory and reported operating results. During all periods presented in the accompanying financial statements, there have been no material adjustments related to a revised estimate of inventory valuations.

Work-in-process and finished products inventories consist of material, labor, outside processing costs and manufacturing overhead. Inventories consist of the following:

	December 31, 2012		December 31, 2011
Raw Materials	$	4,064,317	$	3,563,395
Work-in-process		4,112,478		5,936,578
Finished products		2,966,900		3,863,100
Total	$	11,143,695	$	13,363,073

Accrued Liabilities

The Company estimates accrued liabilities by identifying services performed on the Company’s behalf, estimating the level of service performed and determining the associated cost incurred for such service as of each balance sheet date. Examples of estimated accrued expenses include: (1) Fees paid to contract manufacturers in conjunction with the production of clinical materials. These expenses are normally determined through a contract or purchase order issued by the Company; (2) Service fees paid to organizations for their performance in conducting clinical trials. These expenses are determined by contracts in place for those services and communications with project managers on costs which have been incurred as of each reporting date; and (3) Professional and consulting fees incurred with law firms, audit and accounting service providers and other third party consultants. These expenses are determined by either requesting those service providers to estimate unbilled services at each reporting date for services incurred or tracking costs incurred by service providers under fixed fee arrangements.

The Company has processes in place to estimate the appropriate amounts to record for accrued liabilities, which principally involve the applicable personnel reviewing the services provided. In the event that the Company does not identify certain costs that have begun to be incurred or the Company under or over-estimates the level of services performed or the costs of such services, the reported expenses for that period may be too low or too high. The date on which certain services commence, the level of services performed on or before a given date, and the cost of such services often require the exercise of judgment. The Company makes these judgments based upon the facts and circumstances known at the date of the financial statements.

Income Taxes

Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Valuation allowances are provided, if, based upon the weight of available evidence, it is more likely than not that some or all of the deferred tax assets will not be realized. The Company accounts for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors including, but not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. The Company evaluates this tax position on a quarterly basis. The Company also accrues for potential interest and penalties, related to unrecognized tax benefits in income tax expense.

Depreciation

Depreciation is calculated using the straight-line method over the estimated useful life of the asset as follows:

Classification	Estimated Useful Life
Leasehold improvements	Shorter of the term of the lease or estimated useful life
Equipment	Three to eight years
Furniture and fixtures	Three years

For depreciation of property and equipment, the Company expensed approximately $2,492,000 in the year ended December 31, 2012, $1,117,000 and $1,141,000 in the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, as well as $1,496,000 in the fiscal year ended March 31, 2011. These amounts include depreciation of assets recorded under capitalized lease agreements of approximately $82,000 in the nine months ended December 31, 2010 and $82,000 in the fiscal year ended March31, 2011. Assets recorded under capital leases were fully depreciated at December 31, 2011.

Earnings (Loss) Per Share

Basic earnings (loss) per share is computed by dividing net income (loss) available to common shareholders by the weighted average number of common shares outstanding during the period. Diluted earnings per share is computed by dividing net income available to common shareholders by the weighted-average number of common shares and dilutive common share equivalents then outstanding. Potential common share equivalents consist of restricted stock awards and the incremental common shares issuable upon the exercise of stock options and warrants. Under the treasury stock method, unexercised “in-the-money” stock options are assumed to be exercised at the beginning of the period or at issuance, if later. The assumed proceeds are then used to purchase common shares at the average market price during the period. Share-based payment awards that entitle their holders to receive non-forfeitable dividends before vesting are considered participating securities and are included in the calculation of basic and diluted earnings per share.

A reconciliation of basic and diluted share amounts is as follows:

	Year ended December 31,		Nine Months ended December 31,					Year ended March 31,
	2012		2011			2010		2011
Numerator:
Net income (loss)	$	14,156,037	$	(1,612,625	)	$	1,987,178	$	(43,509	)
Denominator:
Basic weighted average common shares outstanding		30,914,424		30,774,467			30,778,430		30,781,881
Weighted average common stock equivalents from assumed exercise of stock options and restricted stock awards		339,010		—			170,834		—
Diluted weighted average common shares outstanding		31,253,434		30,774,467			30,949,264		30,781,881
Basic net income (loss) per common share	$	0.46	$	(0.05	)	$	0.06	$	(0.00	)
Diluted net income (loss) per common share	$	0.45	$	(0.05	)	$	0.06	$	(0.00	)

At December 31, 2012, there were outstanding options to purchase 2,315,090 shares of the Company’s common stock at a weighted average exercise price of $4.20 per share. For the fiscal year ended December 31, 2012, 1,296,700 shares of the Company’s common stock were excluded from the calculation of diluted earnings per share because the exercise prices of the stock options were greater than or equal to the average price of the common shares, and were therefore anti-dilutive.

At December 31, 2011, there were outstanding options to purchase 2,823,400 shares of the Company’s common stock at a weighted average exercise price of $4.05 per share.

At December 31, 2010, there were outstanding options to purchase 2,566,450 shares of the Company’s common stock at a weighted average exercise price of $4.08 per share. For the nine-month fiscal year ended December 31, 2010, 1,771,100 shares of the Company’s common stock were excluded from the calculation of diluted earnings per share because the exercise prices of the stock options were greater than or equal to the average price of the common shares, and were therefore anti-dilutive.

Diluted weighted average shares outstanding for the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011 do not include the impact of 2,823,400 and 2,580,600 outstanding potential common shares for stock options, respectively, as they would be anti-dilutive. Accordingly, basic and diluted net loss per share are the same for the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011.

Segment Reporting

The Company views its operations, makes decisions regarding how to allocate resources and manages its business as one operating segment. As a result, the financial information disclosed herein represents all of the material financial information related to the Company’s principal operating segment.

The following table represents the Company’s total revenue by geographic area (based on the location of the customer):

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
United States		46	%		48	%		48	%		50	%
Sweden		42	%		44	%		45	%		42	%
Other		12	%		8	%		7	%		8	%
Total		100	%		100	%		100	%		100	%

The following table represents the Company’s total assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	58,356,697	$	44,223,080
Sweden		38,653,466		31,833,734
Total	$	97,010,163	$	76,056,814

The following table represents the Company’s long-lived assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	16,537,804	$	13,380,836
Sweden		14,262,908		15,781,172
Total	$	30,800,712	$	29,162,008

Concentrations of Credit Risk and Significant Customers

Financial instruments that subject the Company to significant concentrations of credit risk primarily consist of cash and cash equivalents, marketable securities and accounts receivable. Per the Company’s investment policy, cash equivalents and marketable securities are invested in financial instruments with high credit ratings and credit exposure to any one issue, issuer (with the exception of U.S. treasury obligations) and type of instrument is limited. At December 31, 2012 and 2011, the Company had no investments associated with foreign exchange contracts, options contracts or other foreign hedging arrangements.

Concentration of credit risk with respect to accounts receivable is limited to customers to whom the Company makes significant sales. While a reserve for the potential write-off of accounts receivable is maintained, the Company has not written off any significant accounts to date. To control credit risk, the Company performs regular credit evaluations of its customers’ financial condition.

Revenue from significant customers as a percentage of the Company’s total revenue is as follows:

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
Orencia® Royalties from Bristol		24	%		37	%		37	%		38	%
Bioprocessing Customer A		42	%		44	%		45	%		42	%

Significant accounts receivable balances as a percentage of the Company’s total trade accounts receivable and royalties and other receivable balances are as follows:

	December 31, 2012			December 31, 2011
Orencia® Royalties from Bristol		31	%		53	%
Bioprocessing Customer A		21	%		31	%
Pfizer		38	%		—

Goodwill, Other Intangible Assets and Acquisitions

Acquisitions

Total consideration transferred for acquisitions (see Note 11) is allocated to the assets acquired and liabilities assumed, if any, based on their fair values at the dates of acquisition. The fair value of identifiable intangible assets is based on detailed valuations that use information and assumptions determined by management. Any excess of purchase price over the fair value of the net tangible and intangible assets acquired is allocated to goodwill. Any excess of the fair value of the net tangible and intangible assets acquired over the purchase price is recognized in the statement of operations. The fair value of contingent consideration includes estimates and judgments made by management regarding the probability that future contingent payments will be made and the extent of royalties to be earned in excess of the defined minimum royalties. Management updates these estimates and the related fair value of contingent consideration at each reporting period. Changes in the fair value of contingent consideration are recorded in the consolidated statements of operations.

The Company uses the income approach to determine the fair value of certain identifiable intangible assets including customer relationships and developed technology. This approach determines fair value by estimating after-tax cash flows attributable to these assets over their respective useful lives and then discounting these after-tax cash flows back to a present value. The Company bases its assumptions on estimates of future cash flows, expected growth rates, expected trends in technology, etc. Discount rates used to arrive at a present value as of the date of acquisition are based on the time value of money and certain industry-specific risk factors.

Goodwill

Goodwill is not amortized and is reviewed for impairment at least annually. There was no evidence of impairment to goodwill at December 31, 2012. There were no goodwill impairment charges during the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 or the fiscal year ended March 31, 2011.

Intangible Assets

Intangible assets are amortized over their useful lives using the estimated economic benefit method, as applicable, and the amortization expense is recorded within cost of product revenue and selling, general and administrative expense in the statements of operations. Intangible assets and their related useful lives are reviewed at least annually to determine if any adverse conditions exist that would indicate the carrying value of these assets may not be recoverable. More frequent impairment assessments are conducted if certain conditions exist, including a change in the competitive landscape, any internal decisions to pursue new or different technology strategies, a loss of a significant customer, or a significant change in the marketplace, including changes in the prices paid for our products or changes in the size of the market for our products. An impairment results if the carrying value of the asset exceeds the estimated fair value of the asset based on the sum of the future undiscounted cash flows expected to result from the use and disposition of the asset. If the estimate of an intangible asset’s remaining useful life is changed, the remaining carrying amount of the intangible asset is amortized prospectively over the revised remaining useful life. The Company continues to believe that its intangible assets are recoverable at December 31, 2012.

Intangible assets consisted of the following at December 31, 2012:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,452,729	$	(360,748	)		8
Patents		240,000		(87,500	)		8
Customer relationships		6,872,383		(934,852	)		8
Total intangible assets	$	8,565,112	$	(1,383,100	)		8

Intangible assets consisted of the following at December 31, 2011:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,413,564	$	(184,402	)		8
Patents		240,000		(57,500	)		8
Customer relationships		6,508,147		(124,570	)		8
Total intangible assets	$	8,161,711	$	(366,472	)		8

Amortization expense for amortized intangible assets was approximately $1,017,000 for the year ended December 31, 2012, $158,000 for the nine-month fiscal year ended December 31, 2011, $134,000 for the nine-month period ended December 31, 2010 and $179,000 for the fiscal year ended March 31, 2011. The Company expects to record amortization expense of approximately $1,000,000 in each of the next five years.

Stock Based Compensation

The Company measures stock-based compensation cost at the grant date based on the estimated fair value of the award, and recognizes it as expense over the employee’s requisite service period on a straight-line basis. The Company records the expense for share-based awards subject to performance-based milestone vesting over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates whether the achievement of a performance-based milestone is probable as of the reporting date. The Company has no awards that are subject to market conditions. The Company recognizes stock-based compensation expense based upon options that are ultimately expected to vest, and accordingly, such compensation expense has been adjusted by an amount of estimated forfeitures.

The Company uses the Black-Scholes option pricing model to calculate the fair value of share-based awards on the grant date. The following assumptions are used in calculating the fair value of share-based awards:

Expected term—The expected term of options granted represents the period of time for which the options are expected to be outstanding. The expected term is presumed to be the midpoint between the vesting date and the end of the contractual term. In addition, for purposes of estimating the expected term, the Company has aggregated all individual option awards into one group as the Company does not expect substantial differences in exercise behavior among its employees.

Expected volatility—The expected volatility is a measure of the amount by which the Company’s stock price is expected to fluctuate during the expected term of options granted. The Company determines the expected volatility based primarily upon the historical volatility of the Company’s common stock over a period commensurate with the option’s expected term, exclusive of any events not reasonably anticipated to recur over the option’s expected term.

Risk-free interest rate—The risk-free interest rate is the implied yield available on U.S. Treasury zero-coupon issues with a remaining term equal to the option’s expected term on the grant date.

Expected dividend yield—The Company has never declared or paid any cash dividends on any of its capital stock and does not expect to do so in the foreseeable future. Accordingly, the Company uses an expected dividend yield of zero to calculate the grant-date fair value of a stock option.

Estimated forfeiture rates—The Company has applied, based on an analysis of its historical forfeitures, annual forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees to all unvested stock options as of December 31, 2012. The Company reevaluates this analysis periodically and adjusts these estimated forfeiture rates as necessary. Ultimately, the Company will only recognize expense for those shares that vest.

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Roll Forward of Fair Value of Contingent Consideration (Detail) (USD $)	12 Months Ended
	Dec. 31, 2012
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Balance at December 31, 2011	$ 2,197,226
Additions
Payments	(35,000)
Changes in fair value	736,850
Balance at December 31, 2012	$ 2,899,076

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Percentage of Accounts Receivable by Significant Customers (Detail) (Accounts Receivable)	Dec. 31, 2012	Dec. 31, 2011
Orencia Royalties from Bristol
Concentration Risk [Line Items]
Accounts receivable, percentage by customer	31.00%	53.00%
Bioprocessing Customer A
Concentration Risk [Line Items]
Accounts receivable, percentage by customer	21.00%	31.00%
Pfizer Inc
Concentration Risk [Line Items]
Accounts receivable, percentage by customer	38.00%

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Commitments and Contingencies - Additional Information (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended						9 Months Ended		12 Months Ended					9 Months Ended	12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012 Building sqft	Jul. 31, 2011 sqft	Mar. 31, 2011	Mar. 31, 2008 sqft	Mar. 31, 2007 sqft	Mar. 31, 2001 sqft	Dec. 31, 2011 Licensing Agreements	Dec. 31, 2010 Licensing Agreements	Dec. 31, 2012 Licensing Agreements	Mar. 31, 2011 Licensing Agreements	Mar. 31, 2010 Licensing Agreements License Fees	Mar. 31, 2011 Licensing Agreements Sub License Fees	Mar. 31, 2010 Licensing Agreements Sub License Fees	Dec. 31, 2011 Licensing Agreements Milestone Payable	Dec. 31, 2012 Lease for three buildings sqft	Dec. 31, 2012 Lease for the fourth building sqft
Commitments and Contingencies [Line Items]
Lease agreement, term												11 years		2 years	5 years	10 years
Lease agreement, space											45,000	56,000		7,350	2,500	25,000									41,000	4,000
Lease agreement, expiration date												May 31, 2023													Jun. 30, 2017	Sep. 30, 2019
Lease agreement, letter of credit issued												$ 200,000
Lease agreement, number buildings leased											4
Operating leases, rent expense									528,000	510,000	2,183,000		686,000
Operating leases, deferred rent liabilities	329,000				15,000				15,000		329,000
Research and development expenses	2,343,000	2,433,000	2,906,000	2,808,000	2,870,000	3,075,000	3,517,000	3,785,000	9,461,960	8,744,548	10,489,811		12,528,819				525,000	343,000	55,000	374,000	500,000	65,000	175,000	500,000
Research and development, financial obligation																			16,000,000
Purchase Orders, Supply Agreements and Other Contractual Obligations	$ 2,872,000										$ 2,872,000

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CONSOLIDATED BALANCE SHEETS (USD $)	Dec. 31, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 29,209,821	$ 11,167,745
Marketable securities	10,845,195	15,421,436
Accounts receivable, less reserve for doubtful accounts of $10,000	4,158,758	2,825,414
Royalties and other receivables	9,130,515	3,206,840
Inventories, net	11,143,695	13,363,073
Deferred tax asset, net	416,580	31,839
Prepaid expenses and other current assets	1,304,887	878,459
Total current assets	66,209,451	46,894,806
Property, plant and equipment, at cost:
Leasehold improvements	5,200,271	5,083,852
Equipment	12,802,978	12,011,154
Furniture and fixtures	1,937,238	1,244,451
Construction in progress	338,814	275,258
Total property, plant and equipment, at cost	20,279,301	18,614,715
Less: Accumulated depreciation	(10,326,840)	(7,877,296)
Property, plant and equipment, net	9,952,461	10,737,419
Long-term deferred tax asset, net	2,557,384
Long-term marketable securities	9,914,855	9,435,350
Intangible assets, net	7,182,012	7,795,239
Goodwill	994,000	994,000
Restricted cash	200,000	200,000
Total assets	97,010,163	76,056,814
Current liabilities:
Accounts payable	2,454,238	1,422,483
Accrued liabilities	8,297,990	6,041,038
Total current liabilities	10,752,228	7,463,521
Deferred tax liability		136,881
Other long-term liabilities	2,133,339	2,469,412
Commitments and contingencies (Note 5)
Stockholders' equity:
Preferred stock, $.01 par value, 5,000,000 shares authorized, no shares issued or outstanding
Common stock, $.01 par value, 40,000,000 shares authorized, 31,195,041 shares at December 31, 2012 and 30,714,757 shares at December 31, 2011 issued and outstanding	311,950	307,148
Additional paid-in capital	187,051,253	184,872,839
Accumulated other comprehensive income	1,911,970	113,627
Accumulated deficit	(105,150,577)	(119,306,614)
Total stockholders' equity	84,124,596	65,987,000
Total liabilities and stockholders' equity	$ 97,010,163	$ 76,056,814

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Income Taxes - Additional Information (Detail) (USD $)	9 Months Ended	12 Months Ended
	Dec. 31, 2011	Dec. 31, 2012	Mar. 31, 2011
Income Taxes [Line Items]
Deferred tax assets from share-based payments		$ 441,000
Valuation allowance increase and decrease	73,000	(10,169,000)	2,227,000
Cumulative pre-tax income position, Year		3 years
Reversed of deferred tax asset valuation allowance		3,021,000
Earnings of foreign subsidiaries permanently reinvest outside the U.S		477,000
Maximum
Income Taxes [Line Items]
Net operating loss and business tax credit carry forwards expiration date		At various dates through December 2032
Available to Reduce Future Federal Income Taxes
Income Taxes [Line Items]
Net operating loss carry forwards		44,678,000
Business tax credit carry forwards		$ 2,160,000

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CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Cash flows from operating activities:
Net income (loss):	$ (1,612,625)	$ 1,987,178	$ 14,156,037	$ (43,509)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization	1,274,597	1,274,247	3,508,592	1,674,528
Stock-based compensation expense	730,136	748,235	1,024,152	1,003,266
Deferred tax expense	15,744		(3,143,268)
Gain on bargain purchase	(427,478)		(314,244)
Loss on revaluation of contingent consideration	28,182		604,133
Loss on disposal of assets	2,826			5,597
Changes in assets and liabilities:
Accounts receivable	3,551,969	(601,141)	(1,211,343)	(689,569)
Royalties and other receivables	(694,238)	(450,600)	(5,923,675)	(216,602)
Inventories	(870,252)	263,570	2,734,239	247,164
Prepaid expenses and other current assets	(190,007)	(708,311)	30,266	986,340
Accounts payable	247,222	(291,824)	1,001,546	(60,404)
Accrued liabilities	243,182	(408,224)	2,083,964	383,237
Long-term liabilities	11,487	(25,447)	(1,110,791)	(58,285)
Net cash provided by operating activities	2,310,745	1,787,683	13,439,608	3,231,763
Cash flows from investing activities:
Purchases of marketable securities	(49,465,924)	(58,095,140)	(39,109,959)	(84,329,731)
Sales of marketable securities	26,290,378
Redemptions of marketable securities	45,624,819	54,225,000	43,214,487	83,650,417
Purchases of property, plant and equipment	(575,455)	(317,982)	(1,263,647)	(524,666)
Net cash provided by (used in) investing activities	(5,010,610)	(4,488,122)	2,840,881	(1,503,980)
Cash flows from financing activities:
Exercise of stock options	25	25,758	1,159,064	6,571
Repurchase and retirement of treasury stock	(330,867)
Principal payments under capital lease obligations		(56,850)		(56,850)
Net cash provided by (used in) financing activities	(330,842)	(31,092)	1,159,064	(50,279)
Effect of exchange rate changes on cash and cash equivalents	(5,092)		602,523
Net increase (decrease) in cash and cash equivalents	(3,035,799)	(2,731,531)	18,042,076	1,677,504
Cash and cash equivalents, beginning of period	14,203,544	12,526,040	11,167,745	12,526,040
Cash and cash equivalents, end of period	11,167,745	9,794,509	29,209,821	14,203,544
Supplemental disclosure of non-cash investing activities:
Income taxes paid			140,000
BioFlash Partners, LLC
Cash flows from investing activities:
Payment for acquisition of business		(300,000)		(300,000)
Novozymes
Cash flows from investing activities:
Payment for acquisition of business	(26,884,428)
Supplemental disclosure of non-cash investing activities:
Contingent consideration transferred in acquisition	$ 1,610,560

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License Agreements - Additional Information (Detail) (USD $)	1 Months Ended	3 Months Ended								9 Months Ended		12 Months Ended		9 Months Ended		12 Months Ended					9 Months Ended		12 Months Ended		1 Months Ended	12 Months Ended									1 Months Ended
	Apr. 30, 2007	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011	Dec. 31, 2011 Licensing Agreements	Dec. 31, 2010 Licensing Agreements	Dec. 31, 2012 Licensing Agreements	Mar. 31, 2011 Licensing Agreements	Mar. 31, 2010 Licensing Agreements License Fees	Mar. 31, 2011 Licensing Agreements Sub License Fees	Mar. 31, 2010 Licensing Agreements Sub License Fees	Dec. 31, 2011 Licensing Agreements Milestone Payable	Dec. 31, 2012 Families of Spinal Muscular Atrophy Licensing Agreements	Mar. 31, 2010 Families of Spinal Muscular Atrophy Licensing Agreements License Fees	Mar. 31, 2010 Families of Spinal Muscular Atrophy Licensing Agreements Sub License Fees	Apr. 30, 2011 Families of Spinal Muscular Atrophy Licensing Agreements Milestone Payable	Dec. 31, 2012 Scripps Research Institute Licensing Agreements	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement Allocated Based on Selling Price of Deliverables	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement Transitional Services	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement Completion of Second Cohort Clinical Trial	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement Clinical Trial Material	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement Clinical Milestone Events	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement First Commercial Sale Milestone Events	Dec. 31, 2012 Pfizer Incorporation Nonsoftware License Arrangement First Clinical Milestone Payment	Jan. 31, 2013 Pfizer Incorporation Nonsoftware License Arrangement Up-front Payment Arrangement
Research and Development Arrangement, Contract to Perform for Others [Line Items]
Payment received under license agreement																																			$ 5,000,000
Total future milestone receivable																											65,000,000					30,000,000	35,000,000	2,000,000
License agreement, revenue recognized																											4,876,000	124,000	76,000	35,000	13,000
Estimated selling price used to allocate consideration																													600,000	275,000	105,000
License Agreement, initial license fee																										300,000
Total future milestone payments																										4,300,000
Common stock, shares issued																										87,464
Common stock, shares issued value																										300,000
Common stock, shares purchased through issuance of warrants	150,000																									150,000
Warrant term	7 years																									7 years
License Agreement termination, written notice period																										90 days
Research and development expenses		2,343,000	2,433,000	2,906,000	2,808,000	2,870,000	3,075,000	3,517,000	3,785,000	9,461,960	8,744,548	10,489,811	12,528,819	525,000	343,000	55,000	374,000	500,000	65,000	175,000	500,000		500,000	175,000	500,000
Research and development, financial obligation																$ 16,000,000						$ 16,000,000
License Agreement, expiration term																						10 years

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Reconciliation of Basic and Diluted Shares Amounts (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Numerator:
Net income (loss)	$ 9,553,000	$ 1,806,000	$ 1,570,000	$ 1,226,000	$ (2,162,000)	$ 605,000	$ (55,000)	$ (2,030,000)	$ (1,612,625)	$ 1,987,178	$ 14,156,037	$ (43,509)
Denominator:
Basic weighted average common shares outstanding	31,132,000	30,948,000	30,845,000	30,730,000	30,715,000	30,797,000	30,812,000	30,782,000	30,774,467	30,778,430	30,914,424	30,781,881
Weighted average common stock equivalents from assumed exercise of stock options and restricted stock awards										170,834	339,010
Diluted weighted average common shares outstanding	31,600,000	31,256,000	31,149,000	31,010,000	30,715,000	30,934,000	30,812,000	30,782,000	30,774,467	30,949,264	31,253,434	30,781,881
Basic net income (loss) per common share	$ 0.31	$ 0.06	$ 0.05	$ 0.04	$ (0.07)	$ 0.02	$ 0.00	$ (0.06)	$ (0.05)	$ 0.06	$ 0.46	$ 0.00
Diluted net income (loss) per common share	$ 0.30	$ 0.06	$ 0.05	$ 0.04	$ (0.07)	$ 0.02	$ 0.00	$ (0.06)	$ (0.05)	$ 0.06	$ 0.45	$ 0.00

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Stockholders' Equity (Tables)

12 Months Ended

Dec. 31, 2012

Stock-Based Compensation Expense

The following table presents stock-based compensation expense in the Company’s consolidated statements of operations:

	Year ended December 31, 2012		Nine Months ended December 31,				Year ended March 31, 2011
			2011		2010 (unaudited)
Cost of product revenue	$	45,000	$	35,000	$	38,000	$	48,000
Research and development		219,000		191,000		164,000		226,000
Selling, general and administrative		760,000		504,000		546,000		729,000
Total	$	1,024,000	$	730,000	$	748,000	$	1,003,000

Estimated Weighted Average Assumptions

The fair value of share-based awards granted during the year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 and the fiscal year ended March 31, 2011 were calculated using the following estimated assumptions:

	Year ended December 31,	Nine Months ended December 31,		Years ended March 31,
	2012	2011	2010	2011
Expected term (years)	6.5	6.5	6.5	6.5
Volatility	49.76% - 53.54%	53.09% - 55.76%	57.58% - 63.60%	55.94% - 63.60%
Risk-free interest rate	0.89% - 1.06%	1.25% - 2.38%	1.81% - 2.62%	1.81% - 2.83%
Expected dividend yield	—	—	—	—

Summary of Option Activity

Information regarding option activity for the year ended December 31, 2012 under the Plans is summarized below:

	Options Outstanding			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term (in years)		Aggregate Intrinsic Value
Options outstanding at December 31, 2011		2,823,400		$	4.05
Granted		368,690			3.65
Exercised		(609,400	)		3.06
Forfeited/cancelled		(267,600	)		4.44
Options outstanding at December 31, 2012		2,315,090		$	4.20		6.16	$	4,854,412
Options exercisable at December 31, 2012		1,447,600		$	4.39		4.96	$	2,783,183
Vested and expected to vest at December 31, 2012 (1)		2,186,609		$	4.21		6.05	$	4,570,615

(1) This represents the number of vested options as of December 31, 2012 plus the number of unvested options expected to vest as of December 31, 2012 based on the unvested outstanding options at December 31, 2012 adjusted for estimated forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees.

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Percentage of Revenue by Geographic Area (Detail) (Total Revenue)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Concentration Risk [Line Items]
Revenues, percentage by country	100.00%	100.00%	100.00%	100.00%
United States
Concentration Risk [Line Items]
Revenues, percentage by country	48.00%	48.00%	46.00%	50.00%
Sweden
Concentration Risk [Line Items]
Revenues, percentage by country	44.00%	45.00%	42.00%	42.00%
Other
Concentration Risk [Line Items]
Revenues, percentage by country	8.00%	7.00%	12.00%	8.00%

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Prepaid Expenses and Other Current Assets (Tables)

12 Months Ended

Dec. 31, 2012

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consist of the following:

	December 31, 2012		December 31, 2011
Equipment maintenance and services		747,273		424,328
Prepaid insurance		365,167		251,418
Interest receivable		140,363		106,695
Clinical and research expenses		15,354		13,714
Other		36,730		82,304
Total	$	1,304,887	$	878,459

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Organization and Nature of Business

12 Months Ended

Dec. 31, 2012

Organization and Nature of Business

1. Organization and Nature of Business

Repligen Corporation (“Repligen” or the “Company”) is a life sciences company that develops, manufactures and markets high-value, consumable bioprocessing products for life sciences companies and biopharmaceutical manufacturing companies worldwide. The Company is a world-leading manufacturer of both native and recombinant forms of Protein A, critical reagents used in biomanufacturing to separate and purify monoclonal antibodies, a type of biologic drug. Repligen also supplies several growth factor products used to increase cell culture productivity during the biomanufacturing process. In the burgeoning area of disposable biomanufacturing technologies, the Company has developed and currently markets a series of OPUS (Open-Platform, User-Specified) chromatography columns for use in clinical-scale manufacturing. The Company generally manufactures and sells Protein A and growth factors to life sciences companies under long-term supply agreements and sells its chromatography columns, as well as media and quality test kits, directly to biopharmaceutical companies or contract manufacturing organizations. Repligen refers to these activities as its bioprocessing business. The Company manufactures its products in production facilities in the United States and Sweden.

Historically, Repligen also conducted activities aimed at developing proprietary therapeutic drug candidates, often with a potential of entering into a collaboration with a larger commercial stage pharmaceutical or biotechnology company in respect of these programs. In addition, the Company has out-licensed certain intellectual property to Bristol-Myers Squibb Company, or Bristol, from which Repligen receives royalties on Bristol’s net sales in the United States of their product Orencia^®. As part of Repligen’s strategic decision in 2012 to focus the Company’s efforts on its core bioprocessing business, the Company scaled back efforts on its clinical development programs and increased its efforts to find collaboration partners to finish their development and, if successful, commercialize these therapeutic drug candidates.

The Company is subject to a number of risks typically associated with companies in the biotechnology industry. These risks principally include the Company’s dependence on key customers, development by the Company or its competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with the FDA and other governmental regulations and approval requirements, as well as the ability to grow the Company’s business and obtain adequate funding to finance this growth.

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CONSOLIDATED BALANCE SHEETS (Parenthetical) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Accounts receivable, reserve for doubtful accounts	$ 10,000	$ 10,000
Preferred stock, par value	$ 0.01	$ 0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued
Preferred stock, shares outstanding
Common stock, par value	$ 0.01	$ 0.01
Common stock, shares authorized	40,000,000	40,000,000
Common stock, shares issued	31,195,041	30,714,757
Common stock, shares outstanding	31,195,041	30,714,757

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Acquisitions

12 Months Ended

Dec. 31, 2012

Acquisitions

11. Acquisitions

Novozymes Biopharma Sweden AB

On December 20, 2011, the Company acquired the Novozymes Biopharma Business from Novozymes, for total consideration transferred of $28,495,000. The terms of the transaction required that the payment be denominated in Euros, but it is reflected here in U.S. dollars for presentation purposes. The Novozymes Acquisition diversified and expanded Repligen’s bioprocessing product offering and customer base while doubling the Company’s manufacturing capacity. The terms of the acquisition included an upfront payment of $26,884,000 and future potential milestone payments totaling up to €4,000,000, if specific sales targets are met for certain products by various dates ending on December 31, 2014 and upon the transfer of manufacturing processes for certain products. This business operates as the Company’s wholly-owned subsidiary, Repligen Sweden AB. The €4,000,000 contingent consideration had an initial probability-weighted fair value at acquisition of $1,611,000.

Consideration Transferred

The Company accounted for the Novozymes Acquisition as the purchase of a business under GAAP. Under the acquisition method of accounting, the assets and certain liabilities of the Novozymes Biopharma Business were recorded as of the acquisition date, at their respective fair values, and consolidated with those of Repligen. The fair value of the net assets acquired was originally estimated to be $28,922,000, which exceeded the total consideration transferred of $28,495,000. Accordingly, the Company recognized the excess of the fair value of the net assets over the purchase price of approximately $427,000 as a gain on bargain purchase. During the year ended December 31, 2012, the fair value of the net assets acquired increased to $29,236,000, due primarily to working capital adjustments on the purchased assets. These adjustments resulted in an additional gain on bargain purchase of $314,000 which was recorded in the year ended December 31, 2012 and is shown separately within income from operations in the consolidated statements of operations.

The Company believes that it was able to acquire the Novozymes Biopharma Business for less than the fair value of its assets because of (i) the Company’s unique position as a market leader in this industry segment and (ii) the seller’s intent to exit this industry segment, which was only a small part of the seller’s overall business and no longer fit its strategy.

The preparation of the valuation to support the fair value of acquired assets and liabilities required the use of significant assumptions and estimates. Critical estimates included, but were not limited to, future expected cash flows, including projected revenues and expenses, and the applicable discount rates. These estimates were based on assumptions that the Company believes to be reasonable. However, actual results may differ from these estimates.

The total consideration transferred follows:

Cash consideration	$	26,445,000
Estimated fair value of contingent consideration		1,611,000
Total consideration transferred	$	28,056,000

The fair value of contingent consideration was determined based upon a probability weighted analysis of expected future milestone payments to be made to the seller. The Company could make payments of up to €4,000,000 if specific sales targets are met for certain products by various dates ending on December 31, 2014 and upon the transfer of manufacturing processes for certain products. The Company recorded a $618,000 increase in the liability for contingent consideration in the year ended December 31, 2012 to reflect updates to the Company’s probability analysis and for the time value of money. At December 31, 2012, $1,322,000 of the liability for contingent consideration is included in current liabilities and $1,033,000 is included in other long-term liabilities in the consolidated balance sheet. The liability will be remeasured at each reporting period until the contingency is resolved.

The Company incurred approximately $1.7 million in transaction costs related to the Novozymes Acquisition. The transaction costs are included in selling, general and administrative expenses in the consolidated statements of operations in the period ended December 31, 2011.

Fair Value of Net Assets Acquired

The following chart summarizes the allocation of the fair value of assets acquired and liabilities assumed:

Accounts receivable	$	5,088,000
Inventory		10,497,000
Prepaid expenses		180,000
Fixed assets		9,089,000
Customer relationships and acquired technology		6,705,000
Deferred tax liability		(198,000	)
Accounts payable and other liabilities assumed		(2,563,000	)
Net assets acquired	$	28,798,000
Less total consideration transferred		(28,056,000	)
Gain on bargain purchase	$	742,000

The Company finalized its fixed asset valuation analysis in the quarter ended September 30, 2012 and the purchase price allocation is now considered final.

BioFlash Partners, LLC

On January 29, 2010, the Company acquired the assets of BioFlash Partners, LLC (“BioFlash”), including a technology platform for the production of pre-packed, “plug and play” chromatography columns for total consideration transferred of $2.6 million. This patented technology enables economical production of chromatography columns in a format that is ready for use in the production of a broad range of biopharmaceuticals, including monoclonal antibodies, vaccines and recombinant proteins. The terms of the acquisition included an upfront payment of $1.8 million and a milestone payment of $300,000 that was made in November 2010.

The Company manufactures and sells these pre-packed columns under the brand name OPUS. OPUS pre-packed chromatography columns have the potential to improve manufacturing efficiencies by reducing time for column packing, set-up and cleaning.

Total consideration transferred was $2,640,000 comprised of cash payments of $2,080,000 and the fair value of contingent consideration of $560,000.

The fair value of contingent consideration was determined based upon a probability weighted analysis of expected future royalty payments to be made to former shareholders of BioFlash. The liability for contingent consideration is included in current and long-term liabilities on the consolidated balance sheets and will be remeasured at each reporting period until the contingency is resolved.

Allocation of Consideration Transferred

The following chart summarizes the allocation of consideration transferred:

Intangible assets subject to amortization	$	1,430,000
Goodwill		994,000
Equipment		216,000
Total	$	2,640,000

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Document and Entity Information (USD $)	12 Months Ended
	Dec. 31, 2012	Feb. 20, 2013	Jun. 30, 2012
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2012
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	FY
Trading Symbol	RGEN
Entity Registrant Name	REPLIGEN CORP
Entity Central Index Key	0000730272
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		31,219,541
Entity Public Float			$ 126,339,916

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Selected Quarterly Financial Data (Unaudited)

12 Months Ended

Dec. 31, 2012

Selected Quarterly Financial Data (Unaudited)

12. Selected Quarterly Financial Data (Unaudited)

The following table contains consolidated statements of operations information for each of the previous eight quarters. The Company believes that the following information reflects all normal recurring adjustments necessary for a fair presentation of the information for the periods presented. The operating results for any quarter are not necessarily indicative of results for any future period.

	December 31, 2012			September 30, 2012			June 30, 2012			March 31, 2012			December 31, 2011			September 30, 2011		June 30, 2011			March 31, 2011
	(in thousands, except per share amounts)
Revenue:
Product revenue	$	9,710		$	11,123		$	11,659		$	9,342		$	3,114		$	5,742	$	4,359		$	3,150
Royalty and other revenue		9,104			3,981			3,865			3,482			4,051			2,889		3,295			2,756
Total revenue		18,814			15,104			15,524			12,824			7,165			8,631		7,654			5,906
Operating expenses:
Cost of product revenue		5,920			6,419			7,345			5,273			1,511			2,093		1,553			1,393
Cost of royalty and other revenue		620			594			537			462			481			418		416			376
Research and development		2,343			2,433			2,906			2,808			2,870			3,075		3,517			3,785
Selling, general and administrative		3,253			3,126			3,418			3,428			4,268			2,493		2,289			2,438
Contingent consideration – fair value adjustments		267			344			—			—			(427	)		—		—			—
Gain on bargain purchase		—			—			—			(314	)		(427	)		—		—			—
Total operating expenses		12,403			12,916			14,206			11,657			8,703			8,079		7,775			7,992
Income (loss) from operations		6,411			2,188			1,318			1,167			(1,538	)		552		(121	)		(2,086	)
Investment income		62			95			29			31			43			53		66			69
Interest expense		(14	)		7			(27	)		(22	)		(28	)		—		—			(13	)
Other income (expense)		(41	)		(500	)		458			109			(623	)		—		—			—
Income (loss) before income taxes		6,418			1,790			1,778			1,285			(2,146	)		605		(55	)		(2,030	)
Income tax provision (benefit)		(3,135	)		(16	)		208			59			16			—		—			—
Net income (loss)	$	9,553		$	1,806		$	1,570		$	1,226		$	(2,162	)	$	605	$	(55	)	$	(2,030	)
Earnings (loss) per share:
Basic	$	0.31		$	0.06		$	0.05		$	0.04		$	(0.07	)	$	0.02	$	(0.00	)	$	(0.06	)
Diluted	$	0.30		$	0.06		$	0.05		$	0.04		$	(0.07	)	$	0.02	$	(0.00	)	$	(0.06	)
Weighted average shares outstanding:
Basic		31,132			30,948			30,845			30,730			30,715			30,797		30,812			30,782
Diluted		31,600			31,256			31,149			31,010			30,715			30,934		30,812			30,782

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CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS) (USD $)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Revenue:
Product revenue	$ 13,215,053	$ 11,810,869	$ 41,834,188	$ 14,961,397
Royalty and other revenue	10,235,194	9,573,770	20,432,348	12,329,627
Total revenue	23,450,247	21,384,639	62,266,536	27,291,024
Operating expenses:
Cost of product revenue	5,157,135	4,186,670	24,957,243	5,579,759
Cost of royalty and other revenue	1,315,315	1,160,775	2,213,004	1,537,666
Research and development	9,461,960	8,744,548	10,489,811	12,528,819
Selling, general and administrative	9,050,382	5,580,215	13,226,732	8,018,851
Contingent consideration - fair value adjustments			610,877
Gain on bargain purchase	(427,478)		(314,244)
Total operating expenses	24,557,314	19,672,208	51,183,423	27,665,095
Income (loss) from operations	(1,107,067)	1,712,431	11,083,113	(374,071)
Investment income	161,053	287,430	218,604	356,729
Interest expense	(27,773)	(12,683)	(56,714)	(26,167)
Other income (expense)	(623,094)		26,403
Income (loss) before income taxes	(1,596,881)	1,987,178	11,271,406	(43,509)
Income tax (benefit) provision	15,744		(2,884,631)
Net income (loss)	(1,612,625)	1,987,178	14,156,037	(43,509)
Earnings (loss) per share:
Basic	$ (0.05)	$ 0.06	$ 0.46	$ 0.00
Diluted	$ (0.05)	$ 0.06	$ 0.45	$ 0.00
Weighted average shares outstanding:
Basic	30,774,467	30,778,430	30,914,424	30,781,881
Diluted	30,774,467	30,949,264	31,253,434	30,781,881
Other comprehensive income (loss):
Unrealized gain on investments	6,338		7,792
Foreign currency translation gain	107,289		1,790,551
Comprehensive income (loss)	$ (1,498,998)	$ 1,987,178	$ 15,954,380	$ (43,509)

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Prepaid Expenses and Other Current Assets

12 Months Ended

Dec. 31, 2012

Prepaid Expenses and Other Current Assets

6. Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets consist of the following:

	December 31, 2012		December 31, 2011
Equipment maintenance and services		747,273		424,328
Prepaid insurance		365,167		251,418
Interest receivable		140,363		106,695
Clinical and research expenses		15,354		13,714
Other		36,730		82,304
Total	$	1,304,887	$	878,459

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Commitments and Contingencies

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies

5. Commitments and Contingencies

Lease Commitments

In 2001, the Company entered into a ten-year lease agreement for approximately 25,000 square feet of space located in Waltham, Massachusetts to be used for its corporate headquarters, manufacturing, research and development, and marketing and administrative operations. In July 2011, the Company amended this agreement to expand the lease to cover approximately 56,000 square feet and to extend the term of the lease by eleven years, which expires on May 31, 2023. In connection with this lease agreement, the Company issued a letter of credit in the amount of $200,000 to the lessor. The letter of credit is collateralized by a certificate of deposit held by the bank that issued the letter of credit. The certificate of deposit is classified as restricted cash in the accompanying consolidated balance sheets.

In 2007, the Company entered into a five-year lease agreement for approximately 2,500 square feet of space in Waltham, Massachusetts to provide for expanded manufacturing operations. Adjacent to this space, the Company entered into a two-year lease in 2008 for approximately 7,350 square feet of additional space to be used for expanded manufacturing and administrative operations. Both of these leases expired on December 31, 2012 and we are now on a month-to-month basis.

Following the completion of the Novozymes Acquisition, the Company now leases four adjacent buildings in Lund, Sweden totaling approximately 45,000 square feet of space used primarily for biologics manufacturing and administrative operations. The lease for three buildings totaling approximately 41,000 square feet expires on June 30, 2017 while the lease for the fourth building with approximately 4,000 square feet of space expires on September 30, 2019.

Obligations under non-cancelable operating leases, including the facility leases discussed above, as of December 31, 2012 are approximately as follows:

Years Ending	Operating Leases
December 31, 2013	$	2,222,000
December 31, 2014		2,222,000
December 31, 2015		2,222,000
December 31, 2016		2,222,000
December 31, 2017		1,655,000
Thereafter		5,611,000
Minimum lease payments	$	16,154,000

Rent expense charged to operations under operating leases was approximately $2,183,000 for the fiscal year ended December 31, 2012, $528,000 and $510,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, and $686,000 for the fiscal year ended March 31, 2011. As of December 31, 2012 and December 31, 2011, the Company had deferred rent liabilities of $329,000 and $15,000, respectively, related to the escalating rent provisions for the Waltham headquarters.

Licensing and Research Agreements

The Company licenses certain technologies that are, or may be, incorporated into its technology under several agreements and also has entered into several clinical research agreements which require the Company to fund certain research projects. Generally, the license agreements require the Company to pay annual maintenance fees and royalties on product sales once a product has been established using the technologies. The Company recorded research and development expenses associated with license agreements of approximately $55,000 for the fiscal year ended December 31, 2012, $525,000 and $343,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, as well as $374,000 for the fiscal year ended March 31, 2011.

In October 2009, the Company entered into an exclusive worldwide commercial license agreement with Families of Spinal Muscular Atrophy (see Note 10). The initial license fee of $500,000 and a related sublicense fee of $175,000 were charged to research and development expenses in the fiscal year ended March 31, 2010. A related sublicense fee of $65,000 was charged to research and development expenses in the fiscal year ended March 31, 2011. A related milestone payment of $500,000 was charged to research and development expenses in the nine month fiscal year ended December 31, 2011. If all milestones are achieved, total financial obligations under this agreement, including milestone payments, sublicense fees, and other charges, could total approximately $16,000,000. Given the uncertain nature of such a development program, the likelihood that products or services will result from the research program is not known at this time.

Purchase Orders, Supply Agreements and Other Contractual Obligations

In the normal course of business, the Company has entered into purchase orders and other agreement with manufacturers, distributors and others. Outstanding obligations at December 31, 2012 of approximately $2,872,000 are expected to be completed within one year.

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Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2012

Obligations Under Non Cancelable Operating Leases

Obligations under non-cancelable operating leases, including the facility leases discussed above, as of December 31, 2012 are approximately as follows:

Years Ending	Operating Leases
December 31, 2013	$	2,222,000
December 31, 2014		2,222,000
December 31, 2015		2,222,000
December 31, 2016		2,222,000
December 31, 2017		1,655,000
Thereafter		5,611,000
Minimum lease payments	$	16,154,000

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Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2012

Use of Estimates

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States (“GAAP”) requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Consolidation

Consolidation

The consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Repligen Europe Limited and Repligen Sweden AB. All significant intercompany accounts and transactions have been eliminated in consolidation.

Foreign Currency

Foreign Currency

The Company translates the assets and liabilities of foreign subsidiaries at rates in effect at the end of the reporting period. Revenues and expenses are translated at average rates in effect during the reporting period. Translation adjustments are included in accumulated other comprehensive income.

Revenue Recognition

Revenue Recognition

Product Sales

The Company generates product revenues from the sale of bioprocessing products to customers in the pharmaceutical and process chromatography industries. The Company recognizes revenue related to product sales upon delivery of the product to the customer as long as there is persuasive evidence of an arrangement, the sales price is fixed or determinable and collection of the related receivable is reasonably assured. Determination of whether these criteria have been met is based on management’s judgments primarily regarding the fixed nature of the fee charged for the product delivered and the collectability of those fees. The Company has a few longstanding customers who comprise the majority of revenue and have excellent payment histories and therefore the Company does not require collateral. The Company has had no significant write-offs of uncollectible invoices in the periods presented.

At the time of sale, the Company also evaluates the need to accrue for warranty and sales returns. The supply agreements the Company has with its customers and related purchase orders identify the terms and conditions of each sale and the price of the goods ordered. Due to the nature of the sales arrangements, inventory produced for sale is tested for quality specifications prior to shipment. Since the product is manufactured to order and in compliance with required specifications prior to shipment, the likelihood of sales return, warranty or other issues is largely diminished. Sales returns and warranty issues are infrequent and have had nominal impact on the Company’s consolidated financial statements historically.

Orencia Royalty

In April 2008, the Company settled its outstanding litigation with Bristol and began recognizing royalty revenue in fiscal year 2009 for Bristol’s net sales in the United States of Orencia^®, which is used in the treatment of rheumatoid arthritis. Pursuant to the settlement with Bristol (see Note 9), the Company recognized royalty revenue of $14,753,000 for the fiscal year ended December 31, 2012, $8,769,000 for the nine-month fiscal year ended December 31, 2011 and $10,251,000 for the fiscal year ended March 31, 2011. Revenue earned from Bristol royalties is recorded in the periods when it is earned based on royalty reports sent by Bristol to the Company. The Company has no continuing obligations to Bristol as a result of this settlement. The Company’s royalty agreement with Bristol provides that the Company will receive such royalty payments from Bristol through December 31, 2013.

Therapeutics Licensing Agreements

Activities under licensing agreements are evaluated in accordance with ASC 605-25 to determine if they represent a multiple element revenue arrangement. The Company identifies the deliverables included within the agreement and evaluates which deliverables represent separate units of accounting. The Company accounts for those components as separate units of accounting if the following two criteria are met:

• The delivered item or items have value to the customer on a stand-alone basis.

• If there is a general right of return relative to the delivered items, delivery or performance of the undelivered items is considered probable and within our control.

Factors considered in this determination include, among other things, whether any other vendors sell the items separately and if the licensee could use the delivered item for its intended purpose without the receipt of the remaining deliverables. If multiple deliverables included in an arrangement are separable into different units of accounting, the Company allocates the arrangement consideration to those units of accounting. The amount of allocable arrangement consideration is limited to amounts that are fixed or determinable. Arrangement consideration is allocated at the inception of the arrangement to the identified units of accounting based on their relative selling price. Revenue is recognized for each unit of accounting when the appropriate revenue recognition criteria are met.

Future milestone payments, if any, under a license agreement will be recognized under the provisions of ASC 605-28, which the Company adopted on January 1, 2011. The Company has elected to recognize a payment that is contingent upon the achievement of a substantive milestone in its entirety in the period in which the milestone is achieved. A milestone is substantive if:

• It can only be achieved based in whole or in part on either (1) the Company’s performance or (2) on the occurrence of a specific outcome resulting from the Company’s performance;

• There is substantive uncertainty at the date an arrangement is entered into that the event will be achieved; and

• It would result in additional payments being due to the entity.

The Company believes that the clinical milestone payments pursuant to the license agreement with Pfizer, Inc. (“Pfizer”), as described in Note 10, are substantive and thus will be recognized when achieved. The commercial milestone payments and royalty payments received under license agreements, if any, will be recognized as revenue when they are earned.

Research and Development Agreements

In the fiscal year ended December 31, 2012, the Company recognized $803,000 of revenue from sponsored research and development projects under agreements with the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, GoFar, and the Friedreich’s Ataxia Research Alliance.

For the nine-month fiscal year ended December 31, 2011, the Company recognized $1,466,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, the European Friedrich’s Ataxia Consortium for Translational Studies, Go Friedreich’s Ataxia Research (“GoFar”), and the Friedreich’s Ataxia Research Alliance. For the nine-month period ended December 31, 2010, the Company recognized $1,102,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. For the nine months ended December 31, 2010, the Company also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

In the fiscal year ended March 31, 2011, the Company recognized $1,346,000 of revenue from sponsored research and development projects under agreements with the Muscular Dystrophy Association, the National Institutes of Health / Scripps Research Institute, GoFar, and the Friedreich’s Ataxia Research Alliance. During the year ended March 31, 2011, the Company also recognized approximately $733,000 in one-time grants under the Qualifying Therapeutic Discovery Project Program, which was created in March 2010 as part of the Patient Protection and Affordability Care Act.

Research revenue is recognized when the expense has been incurred and services have been performed. Determination of which costs incurred qualify for reimbursement under the terms of the Company’s contractual agreements and the timing of when such costs were incurred involves the judgment of management. The Company’s calculations are based upon the agreed-upon terms as stated in the arrangements. However, should the estimated calculations change or be challenged by other parties to the agreements, research revenue may be adjusted in subsequent periods. The calculations have not historically changed or been challenged and the Company does not anticipate any subsequent change in its revenue related to sponsored research and development projects.

There have been no material changes to the Company’s initial estimates related to revenue recognition in any periods presented in the accompanying consolidated financial statements.

Risks and Uncertainties

Risks and Uncertainties

The Company evaluates its operations periodically to determine if any risks and uncertainties exist that could impact its operations in the near term. The Company does not believe that there are any significant risks which have not already been disclosed in the consolidated financial statements. A loss of certain suppliers could temporarily disrupt operations, although alternate sources of supply exist for these items. The Company has mitigated these risks by working closely with key suppliers, identifying alternate sources and developing contingency plans.

Cash, Cash Equivalents and Marketable Securities

Cash, Cash Equivalents and Marketable Securities

At December 31, 2012 and December 31, 2011, the Company’s investments included money market funds as well as short-term and long-term marketable securities. Marketable securities are investments with original maturities of greater than 90 days. Long-term marketable securities are securities with maturities of greater than one year. The average remaining contractual maturity of marketable securities at December 31, 2012 is approximately 9.9 months.

Investments in debt securities consisted of the following at December 31, 2012:

	December 31, 2012
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	2,000,897	$	353	$	(7	)	$	2,001,243
Corporate and other debt securities		8,835,098		8,854		—			8,843,952
		10,835,995		9,207		(7	)		10,845,195
Long-term marketable securities:
U.S. Government and agency securities		5,198,264		2,747		—			5,201,011
Corporate and other debt securities		4,711,679		3,525		(1,360	)		4,713,844
		9,909,943		6,272		(1,360	)		9,914,855
Total	$	20,745,938	$	15,479	$	(1,367	)	$	20,760,050

At December 31, 2012, the Company’s investments included seven debt securities in unrealized loss positions with a total unrealized loss of approximately $1,000 and a total fair market value of approximately $2,667,000. All investments with gross unrealized losses have been in unrealized loss positions for less than 12 months. The unrealized losses were caused primarily by current economic and market conditions. There was no change in the credit risk of the securities. The Company does not intend to sell any investments in an unrealized loss position and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases. There were no realized gains or losses on the investments for the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011 or the fiscal year ended March 31, 2011.

Investments in debt securities consisted of the following at December 31, 2011:

	December 31, 2011
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	8,373,355	$	3,126	$	(233	)	$	8,376,248
Corporate and other debt securities		7,046,222		3,336		(4,370	)		7,045,188
		15,419,577		6,462		(4,603	)		15,421,436
Long-term marketable securities:
U.S. Government and agency securities		8,399,428		2,223		(91	)		8,401,560
Corporate and other debt securities		1,031,443		2,347		—			1,033,790
		9,430,871		4,570		(91	)		9,435,350
Total	$	24,850,448	$	11,032	$	(4,694	)	$	24,856,786

The contractual maturities of debt securities at December 31, 2012 were as follows:

	Amortized Cost		Fair Value
Due in 1 year or less	$	10,835,995	$	10,845,195
Due in 1 to 2 years		9,909,943		9,914,855
	$	20,745,938	$	20,760,050

Fair Value Measurement

Fair Value Measurement

In determining the fair value of its assets and liabilities, the Company uses various valuation approaches. The Company employs a hierarchy for inputs used in measuring fair value that maximizes the use of observable inputs and minimizes the use of unobservable inputs by requiring that observable inputs be used when available. Observable inputs are inputs that market participants would use in pricing the asset or liability based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the asset or liability and are developed based on the best information available in the circumstances. The fair value hierarchy is broken down into three levels based on the source of inputs as follows:

Level 1	—	Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access.
Level 2	—	Valuations based on quoted prices for similar assets or liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active and models for which all significant inputs are observable, either directly or indirectly.
Level 3	—	Valuations based on inputs that are unobservable and significant to the overall fair value measurement.

The availability of observable inputs can vary among the various types of financial assets and liabilities. To the extent that the valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. In certain cases, the inputs used to measure fair value may fall into different levels of the fair value hierarchy. In such cases, for financial statement disclosure purposes, the level in the fair value hierarchy within which the fair value measurement is categorized is based on the lowest level input that is significant to the overall fair value measurement.

The Company’s fixed income investments are comprised of obligations of U.S. government agencies, corporate debt securities and other interest bearing securities. These investments have been initially valued at the transaction price and subsequently valued, at the end of each reporting period, utilizing third party pricing services or other market observable data. The pricing services utilize industry standard valuation models, including both income and market based approaches and observable market inputs to determine value. These observable market inputs include reportable trades, benchmark yields, credit spreads, broker/dealer quotes, bids, offers, current spot rates and other industry and economic events. The Company validates the prices provided by third party pricing services by reviewing their pricing methods and matrices, obtaining market values from other pricing sources, analyzing pricing data in certain instances and confirming that the relevant markets are active. After completing its validation procedures, the Company did not adjust or override any fair value measurements provided by the pricing services as of December 31, 2012.

The following fair value hierarchy table presents information about each major category of the Company’s assets measured at fair value on a recurring basis as of December 31, 2012:

	Fair value measurement at reporting date using:
	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Total
Assets:
Money market funds	$	7,891,062	$	—	$	—	$	7,891,062
U.S. Government and agency securities		2,901,209		5,201,011		—		8,102,220
Corporate and other debt securities		—		13,557,796		—		13,557,796
Total	$	10,792,271	$	18,758,807	$	—	$	29,551,078

The Company has no other assets or liabilities for which fair value measurement is either required or has been elected to be applied, other than the liabilities for contingent consideration recorded in connection with the Novozymes Acquisition and the acquisition of the assets of BioFlash Partners, LLC (“BioFlash”). The contingent consideration related to Novozymes is valued using management’s estimates of expected future milestone payments based upon a probability weighted analysis of amounts to be paid to Novozymes Denmark. The contingent consideration related to BioFlash is valued using management’s estimates of royalties to be paid to the former shareholders of BioFlash based on sales of the acquired assets. These valuations are Level 3 valuations as the primary inputs are unobservable. Changes in the fair value of contingent consideration in the year ended December 31, 2012 are primarily attributable to changes in the probability of the Company making certain contingent payments. The following table provides a roll forward of the fair value of the contingent consideration:

Balance at December 31, 2011	$	2,197,226
Additions		—
Payments		(35,000	)
Changes in fair value		736,850
Balance at December 31, 2012	$	2,899,076

There were no remeasurements to fair value during the year ended December 31, 2012 of financial assets and liabilities that are not measured at fair value on a recurring basis.

Inventories

Inventories

Inventories relate to the Company’s bioprocessing business. The Company values inventory at cost or, if lower, fair market value, using the first-in, first-out method. The Company reviews its inventories at least quarterly and records a provision for excess and obsolete inventory based on its estimates of expected sales volume, production capacity and expiration dates of raw materials, work-in process and finished products. Expected sales volumes are determined based on supply forecasts provided by key customers for the next three to 12 months. The Company writes down inventory that has become obsolete, inventory that has a cost basis in excess of its expected net realizable value, and inventory in excess of expected requirements to cost of product revenue. Manufacturing of bioprocessing finished goods is done to order and tested for quality specifications prior to shipment. Reserves for excess and obsolete inventory were $154,000 and $149,000 as of December 31, 2012 and 2011, respectively. At both December 31, 2010 and March 31, 2011, reserves for excess and obsolete inventory were $50,000.

A change in the estimated timing or amount of demand for the Company’s products could result in additional provisions for excess inventory quantities on hand. Any significant unanticipated changes in demand or unexpected quality failures could have a significant impact on the value of inventory and reported operating results. During all periods presented in the accompanying financial statements, there have been no material adjustments related to a revised estimate of inventory valuations.

Work-in-process and finished products inventories consist of material, labor, outside processing costs and manufacturing overhead. Inventories consist of the following:

	December 31, 2012		December 31, 2011
Raw Materials	$	4,064,317	$	3,563,395
Work-in-process		4,112,478		5,936,578
Finished products		2,966,900		3,863,100
Total	$	11,143,695	$	13,363,073

Accrued Liabilities

Accrued Liabilities

The Company estimates accrued liabilities by identifying services performed on the Company’s behalf, estimating the level of service performed and determining the associated cost incurred for such service as of each balance sheet date. Examples of estimated accrued expenses include: (1) Fees paid to contract manufacturers in conjunction with the production of clinical materials. These expenses are normally determined through a contract or purchase order issued by the Company; (2) Service fees paid to organizations for their performance in conducting clinical trials. These expenses are determined by contracts in place for those services and communications with project managers on costs which have been incurred as of each reporting date; and (3) Professional and consulting fees incurred with law firms, audit and accounting service providers and other third party consultants. These expenses are determined by either requesting those service providers to estimate unbilled services at each reporting date for services incurred or tracking costs incurred by service providers under fixed fee arrangements.

The Company has processes in place to estimate the appropriate amounts to record for accrued liabilities, which principally involve the applicable personnel reviewing the services provided. In the event that the Company does not identify certain costs that have begun to be incurred or the Company under or over-estimates the level of services performed or the costs of such services, the reported expenses for that period may be too low or too high. The date on which certain services commence, the level of services performed on or before a given date, and the cost of such services often require the exercise of judgment. The Company makes these judgments based upon the facts and circumstances known at the date of the financial statements.

Income Taxes

Income Taxes

Deferred taxes are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Valuation allowances are provided, if, based upon the weight of available evidence, it is more likely than not that some or all of the deferred tax assets will not be realized. The Company accounts for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors including, but not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. The Company evaluates this tax position on a quarterly basis. The Company also accrues for potential interest and penalties, related to unrecognized tax benefits in income tax expense.

Depreciation

Depreciation

Depreciation is calculated using the straight-line method over the estimated useful life of the asset as follows:

Classification	Estimated Useful Life
Leasehold improvements	Shorter of the term of the lease or estimated useful life
Equipment	Three to eight years
Furniture and fixtures	Three years

For depreciation of property and equipment, the Company expensed approximately $2,492,000 in the year ended December 31, 2012, $1,117,000 and $1,141,000 in the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, as well as $1,496,000 in the fiscal year ended March 31, 2011. These amounts include depreciation of assets recorded under capitalized lease agreements of approximately $82,000 in the nine months ended December 31, 2010 and $82,000 in the fiscal year ended March31, 2011. Assets recorded under capital leases were fully depreciated at December 31, 2011.

Earnings (Loss) Per Share

Earnings (Loss) Per Share

Basic earnings (loss) per share is computed by dividing net income (loss) available to common shareholders by the weighted average number of common shares outstanding during the period. Diluted earnings per share is computed by dividing net income available to common shareholders by the weighted-average number of common shares and dilutive common share equivalents then outstanding. Potential common share equivalents consist of restricted stock awards and the incremental common shares issuable upon the exercise of stock options and warrants. Under the treasury stock method, unexercised “in-the-money” stock options are assumed to be exercised at the beginning of the period or at issuance, if later. The assumed proceeds are then used to purchase common shares at the average market price during the period. Share-based payment awards that entitle their holders to receive non-forfeitable dividends before vesting are considered participating securities and are included in the calculation of basic and diluted earnings per share.

A reconciliation of basic and diluted share amounts is as follows:

	Year ended December 31,		Nine Months ended December 31,					Year ended March 31,
	2012		2011			2010		2011
Numerator:
Net income (loss)	$	14,156,037	$	(1,612,625	)	$	1,987,178	$	(43,509	)
Denominator:
Basic weighted average common shares outstanding		30,914,424		30,774,467			30,778,430		30,781,881
Weighted average common stock equivalents from assumed exercise of stock options and restricted stock awards		339,010		—			170,834		—
Diluted weighted average common shares outstanding		31,253,434		30,774,467			30,949,264		30,781,881
Basic net income (loss) per common share	$	0.46	$	(0.05	)	$	0.06	$	(0.00	)
Diluted net income (loss) per common share	$	0.45	$	(0.05	)	$	0.06	$	(0.00	)

At December 31, 2012, there were outstanding options to purchase 2,315,090 shares of the Company’s common stock at a weighted average exercise price of $4.20 per share. For the fiscal year ended December 31, 2012, 1,296,700 shares of the Company’s common stock were excluded from the calculation of diluted earnings per share because the exercise prices of the stock options were greater than or equal to the average price of the common shares, and were therefore anti-dilutive.

At December 31, 2011, there were outstanding options to purchase 2,823,400 shares of the Company’s common stock at a weighted average exercise price of $4.05 per share.

At December 31, 2010, there were outstanding options to purchase 2,566,450 shares of the Company’s common stock at a weighted average exercise price of $4.08 per share. For the nine-month fiscal year ended December 31, 2010, 1,771,100 shares of the Company’s common stock were excluded from the calculation of diluted earnings per share because the exercise prices of the stock options were greater than or equal to the average price of the common shares, and were therefore anti-dilutive.

Diluted weighted average shares outstanding for the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011 do not include the impact of 2,823,400 and 2,580,600 outstanding potential common shares for stock options, respectively, as they would be anti-dilutive. Accordingly, basic and diluted net loss per share are the same for the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011.

Segment Reporting

Segment Reporting

The Company views its operations, makes decisions regarding how to allocate resources and manages its business as one operating segment. As a result, the financial information disclosed herein represents all of the material financial information related to the Company’s principal operating segment.

The following table represents the Company’s total revenue by geographic area (based on the location of the customer):

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
United States		46	%		48	%		48	%		50	%
Sweden		42	%		44	%		45	%		42	%
Other		12	%		8	%		7	%		8	%
Total		100	%		100	%		100	%		100	%

The following table represents the Company’s total assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	58,356,697	$	44,223,080
Sweden		38,653,466		31,833,734
Total	$	97,010,163	$	76,056,814

The following table represents the Company’s long-lived assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	16,537,804	$	13,380,836
Sweden		14,262,908		15,781,172
Total	$	30,800,712	$	29,162,008

Concentrations of Credit Risk and Significant Customers

Concentrations of Credit Risk and Significant Customers

Financial instruments that subject the Company to significant concentrations of credit risk primarily consist of cash and cash equivalents, marketable securities and accounts receivable. Per the Company’s investment policy, cash equivalents and marketable securities are invested in financial instruments with high credit ratings and credit exposure to any one issue, issuer (with the exception of U.S. treasury obligations) and type of instrument is limited. At December 31, 2012 and 2011, the Company had no investments associated with foreign exchange contracts, options contracts or other foreign hedging arrangements.

Concentration of credit risk with respect to accounts receivable is limited to customers to whom the Company makes significant sales. While a reserve for the potential write-off of accounts receivable is maintained, the Company has not written off any significant accounts to date. To control credit risk, the Company performs regular credit evaluations of its customers’ financial condition.

Revenue from significant customers as a percentage of the Company’s total revenue is as follows:

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
Orencia® Royalties from Bristol		24	%		37	%		37	%		38	%
Bioprocessing Customer A		42	%		44	%		45	%		42	%

Significant accounts receivable balances as a percentage of the Company’s total trade accounts receivable and royalties and other receivable balances are as follows:

	December 31, 2012			December 31, 2011
Orencia® Royalties from Bristol		31	%		53	%
Bioprocessing Customer A		21	%		31	%
Pfizer		38	%		—

Goodwill, Other Intangible Assets and Acquisitions

Goodwill, Other Intangible Assets and Acquisitions

Acquisitions

Total consideration transferred for acquisitions (see Note 11) is allocated to the assets acquired and liabilities assumed, if any, based on their fair values at the dates of acquisition. The fair value of identifiable intangible assets is based on detailed valuations that use information and assumptions determined by management. Any excess of purchase price over the fair value of the net tangible and intangible assets acquired is allocated to goodwill. Any excess of the fair value of the net tangible and intangible assets acquired over the purchase price is recognized in the statement of operations. The fair value of contingent consideration includes estimates and judgments made by management regarding the probability that future contingent payments will be made and the extent of royalties to be earned in excess of the defined minimum royalties. Management updates these estimates and the related fair value of contingent consideration at each reporting period. Changes in the fair value of contingent consideration are recorded in the consolidated statements of operations.

The Company uses the income approach to determine the fair value of certain identifiable intangible assets including customer relationships and developed technology. This approach determines fair value by estimating after-tax cash flows attributable to these assets over their respective useful lives and then discounting these after-tax cash flows back to a present value. The Company bases its assumptions on estimates of future cash flows, expected growth rates, expected trends in technology, etc. Discount rates used to arrive at a present value as of the date of acquisition are based on the time value of money and certain industry-specific risk factors.

Goodwill

Goodwill is not amortized and is reviewed for impairment at least annually. There was no evidence of impairment to goodwill at December 31, 2012. There were no goodwill impairment charges during the fiscal year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 or the fiscal year ended March 31, 2011.

Intangible Assets

Intangible assets are amortized over their useful lives using the estimated economic benefit method, as applicable, and the amortization expense is recorded within cost of product revenue and selling, general and administrative expense in the statements of operations. Intangible assets and their related useful lives are reviewed at least annually to determine if any adverse conditions exist that would indicate the carrying value of these assets may not be recoverable. More frequent impairment assessments are conducted if certain conditions exist, including a change in the competitive landscape, any internal decisions to pursue new or different technology strategies, a loss of a significant customer, or a significant change in the marketplace, including changes in the prices paid for our products or changes in the size of the market for our products. An impairment results if the carrying value of the asset exceeds the estimated fair value of the asset based on the sum of the future undiscounted cash flows expected to result from the use and disposition of the asset. If the estimate of an intangible asset’s remaining useful life is changed, the remaining carrying amount of the intangible asset is amortized prospectively over the revised remaining useful life. The Company continues to believe that its intangible assets are recoverable at December 31, 2012.

Intangible assets consisted of the following at December 31, 2012:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,452,729	$	(360,748	)		8
Patents		240,000		(87,500	)		8
Customer relationships		6,872,383		(934,852	)		8
Total intangible assets	$	8,565,112	$	(1,383,100	)		8

Intangible assets consisted of the following at December 31, 2011:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,413,564	$	(184,402	)		8
Patents		240,000		(57,500	)		8
Customer relationships		6,508,147		(124,570	)		8
Total intangible assets	$	8,161,711	$	(366,472	)		8

Amortization expense for amortized intangible assets was approximately $1,017,000 for the year ended December 31, 2012, $158,000 for the nine-month fiscal year ended December 31, 2011, $134,000 for the nine-month period ended December 31, 2010 and $179,000 for the fiscal year ended March 31, 2011. The Company expects to record amortization expense of approximately $1,000,000 in each of the next five years.

Stock Based Compensation

Stock Based Compensation

The Company measures stock-based compensation cost at the grant date based on the estimated fair value of the award, and recognizes it as expense over the employee’s requisite service period on a straight-line basis. The Company records the expense for share-based awards subject to performance-based milestone vesting over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates whether the achievement of a performance-based milestone is probable as of the reporting date. The Company has no awards that are subject to market conditions. The Company recognizes stock-based compensation expense based upon options that are ultimately expected to vest, and accordingly, such compensation expense has been adjusted by an amount of estimated forfeitures.

The Company uses the Black-Scholes option pricing model to calculate the fair value of share-based awards on the grant date. The following assumptions are used in calculating the fair value of share-based awards:

Expected term—The expected term of options granted represents the period of time for which the options are expected to be outstanding. The expected term is presumed to be the midpoint between the vesting date and the end of the contractual term. In addition, for purposes of estimating the expected term, the Company has aggregated all individual option awards into one group as the Company does not expect substantial differences in exercise behavior among its employees.

Expected volatility—The expected volatility is a measure of the amount by which the Company’s stock price is expected to fluctuate during the expected term of options granted. The Company determines the expected volatility based primarily upon the historical volatility of the Company’s common stock over a period commensurate with the option’s expected term, exclusive of any events not reasonably anticipated to recur over the option’s expected term.

Risk-free interest rate—The risk-free interest rate is the implied yield available on U.S. Treasury zero-coupon issues with a remaining term equal to the option’s expected term on the grant date.

Expected dividend yield—The Company has never declared or paid any cash dividends on any of its capital stock and does not expect to do so in the foreseeable future. Accordingly, the Company uses an expected dividend yield of zero to calculate the grant-date fair value of a stock option.

Estimated forfeiture rates—The Company has applied, based on an analysis of its historical forfeitures, annual forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees to all unvested stock options as of December 31, 2012. The Company reevaluates this analysis periodically and adjusts these estimated forfeiture rates as necessary. Ultimately, the Company will only recognize expense for those shares that vest.

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Royalty Arrangement with Bristol Myers Squibb Company ("Bristol")

12 Months Ended

Dec. 31, 2012

Royalty Arrangement with Bristol Myers Squibb Company ("Bristol")

9. Royalty Arrangement with Bristol Myers Squibb Company (“Bristol”)

In 2008, the Company together with the University of Michigan entered into a settlement agreement with Bristol related to alleged patent infringement of a certain patent related to the treatment of rheumatoid arthritis. The settlement provides for Bristol to pay royalties on the United States net sales of Orencia^® for any clinical indication at a rate of 1.8% for the first $500 million of annual net sales, 2.0% for the next $500 million of annual net sales and 4% of annual net sales in excess of $1 billion for each year from January 1, 2008 until December 31, 2013.

Pursuant to the Bristol Settlement, the Company recognized royalty revenue of $14,753,000 for the year ended December 31, 2012, $8,769,000 and $7,739,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, and $10,251,000 for the fiscal year ended March 31, 2011.

The Company must also remit to the University of Michigan 15% of all royalty revenue received from Bristol. Royalty expense was $2,213,000 for the year ended December 31, 2012, $1,315,000 and $1,161,000 for the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010, respectively, and $1,537,000 for the fiscal year ended March 31, 2011. Royalty expense is included on the statements of operations under the line item “Cost of royalty and other revenue.”

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Acquisitions - Additional Information (Detail)	12 Months Ended
	Dec. 31, 2012 USD ($)	Dec. 31, 2012 Novozymes Biopharma Sweden Ab USD ($)	Dec. 31, 2011 Novozymes Biopharma Sweden Ab USD ($)	Dec. 20, 2011 Novozymes Biopharma Sweden Ab USD ($)	Dec. 20, 2011 Novozymes Biopharma Sweden Ab EUR (€)	Dec. 20, 2011 Novozymes Biopharma Sweden Ab Up Front Payment USD ($)	Dec. 20, 2011 Novozymes Biopharma Sweden Ab Milestone Payment Arrangement EUR (€)	Dec. 31, 2012 Bio Flash Partners Limited Liability Company USD ($)	Jan. 29, 2010 Bio Flash Partners Limited Liability Company USD ($)	Jan. 29, 2010 Bio Flash Partners Limited Liability Company Milestone Payment Arrangement USD ($)
Business Acquisition [Line Items]
Business acquisition, consideration transferred		$ 28,056,000		$ 28,495,000				$ 2,640,000	$ 2,600,000
Business acquisition, contingent Payment						26,884,000	4,000,000			300,000
Business acquisition, probability-weighted fair value of contingent consideration				1,611,000	4,000,000
Fair Value of net assets acquired		29,236,000	28,922,000
Gain on bargain purchase		314,000	427,000
Business acquisition, Increase in contingent liability	618,000
Contingent consideration, current	1,322,000
Contingent consideration, non-current	1,033,000
Acquisition related costs incurred			1,700,000
Business acquisition, upfront payment				26,445,000				2,080,000	1,800,000
Estimated fair value of contingent consideration				$ 1,611,000				$ 560,000

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Accrued Liabilities

12 Months Ended

Dec. 31, 2012

Accrued Liabilities

7. Accrued Liabilities

Accrued liabilities consist of the following:

	December 31, 2012		December 31, 2011
Employee compensation	$	3,634,839	$	2,741,738
Royalty and license fees		1,459,680		499,776
Contingent consideration		1,376,877		35,000
Unearned revenue		599,120		469,046
Professional fees		418,800		871,086
VAT liabilities		98,162		566,542
Research and development		18,300		142,695
Other accrued expenses		692,212		715,155
Total	$	8,297,990	$	6,041,038

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Employee Benefit Plans

12 Months Ended

Dec. 31, 2012

Employee Benefit Plans

8. Employee Benefit Plans

In the U.S., the Repligen Corporation 401(k) Savings and Retirement Plan (the “401(k) Plan”) is a qualified defined contribution plan in accordance with Section 401(k) of the Internal Revenue Code. All U.S. employees over the age of 21 are eligible to make pre-tax contributions up to a specified percentage of their compensation. Under the 401(k) Plan, the Company may, but is not obligated to match a portion of the employees’ contributions up to a defined maximum. The match is calculated on a calendar year basis. The Company matched approximately $103,000 for the year ended December 31, 2012, $102,000 for the nine-month fiscal year ended December 31, 2011, and $108,000 for both the nine-month period ended December 31, 2010 and the year ended March 31, 2011.

In Sweden, the Company contributes to a government-mandated occupational pension plan that is a qualified defined contribution plan. All employees in Sweden are eligible for this pension plan. The Company pays premiums to a third party occupational pension specialist who administers the pension plan. These premiums are based on various factors including each employee’s age, salary, employment history and selected benefits in the pension plan. When an employee terminates or retires, these premium payments cease for that employee and the Company has no further pension-related obligations for that employee. For the fiscal year ended December 31, 2012, the Company contributed approximately $532,000 to the pension plan. For the period from the completion of the Novozymes Acquisition on December 20, 2011 to December 31, 2011, the Company contributed approximately $10,000 to the pension plan.

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License Agreements

12 Months Ended

Dec. 31, 2012

License Agreements

10. License Agreements

Pfizer

On December 28, 2012, the Company entered into an exclusive worldwide outlicensing agreement (the “License Agreement”) with Pfizer to advance the SMA program, which is led by RG3039 and also includes backup compounds and enabling technologies. Under the terms of the License Agreement, the Company received a $5 million upfront payment on January 22, 2013 and is entitled to receive up to $65 million in potential future milestone payments, a portion of which may be owed to third parties. These potential payments are approximately equally divided between milestones related to clinical development and initial commercial sales in specific geographies. In addition, the Company is entitled to receive royalties on any future sales of RG3039 or any SMA compounds developed under the License Agreement. The License Agreement also provides for tiered and increasing royalty rates which begin in the high single-digits for RG-3039 or lesser amounts for any backup compounds developed under the License Agreement. The Company’s receipt of these royalties is subject to an obligation under an existing in-license agreement and other customary offsets and deductions. Royalties are payable, on a country-by-country basis, for a duration based upon the later of (a) expiration of the licensed patent(s) or (b) a predetermined time after the first commercial sale of the first such product in such country.

Pursuant to the License Agreement, Pfizer will assume virtually all of the costs associated with completing the required clinical trials for the SMA program as well as obtaining FDA approval of the respective NDA. The Company is obligated to conduct additional activities in support of this program, which include completion of the second cohort of the ongoing Phase I trial and supporting the transition of the program to Pfizer. The Company will also provide specific technology transfer services to Pfizer who will then assume full responsibility for the SMA program moving forward, including the conduct of any registration trials necessary for any product approvals. The Company expects to complete its obligation with respect to this program in the first half of 2013. Pfizer may terminate the license agreement at any time for convenience. There are no refund provisions in the License Agreement.

Activities under this agreement were evaluated in accordance with ASC 605-25 to determine if they represented a multiple element revenue arrangement. The Company identified the following deliverables in the Pfizer agreement:

• An exclusive license to research, develop, manufacture, commercialize and use RG3039 and backup compounds for the treatment of SMA and other disorders (the “License”);

• Research and development services designed to transition the SMA program to Pfizer pursuant to a transition plan (the “Transition Services”) ;

• The completion of the second cohort of a phase I clinical trial that was underway at the time the License Agreement was signed; and

• An inventory of RG3039, that could be used in clinical development, specifically to complete the phase I clinical trial, referenced immediately above (the “Clinical Trial Material”).

The deliverables outlined above were deemed to have stand-alone value and to meet the criteria to be accounted for as separate units of accounting. Factors considered in this determination included, among other things, whether any other vendors sell the items separately or whether or not Pfizer had the ability to resell and if Pfizer could use the delivered item for its intended purpose without the receipt of the remaining deliverables. The amount of allocable arrangement consideration is limited to amounts that are fixed or determinable. Arrangement consideration is allocated at the inception of the arrangement to the identified units of accounting based on their relative selling price.

The Company identified the arrangement consideration to allocate among the units of accounting as the $5.0 million non-refundable up-front payment and excluded the potential milestone payments provided for in the License Agreement from the arrangement consideration as they were not considered fixed or determinable at the time the License Agreement was signed. Because Repligen had not sold these items on a standalone basis previously, there was no vendor-specific objective evidence of selling price. Furthermore, the Company did not have detailed third-party evidence of selling price, and as a result used a best estimate of selling price for each item. In determining these prices, the Company considered what it would be willing to sell the items for on a standalone basis, what the market would bear for such items and what another party might charge for these items.

The Company used a discounted cash flow analysis to determine the value of the license. Key assumptions in the analysis included: the estimated market size for a compound targeted at SMA, the estimated remaining costs of development and time to commercialization, and the probability of successfully developing and commercializing the program. A change in the key assumptions used to determine best estimate of selling price for each of the deliverables would not have a significant effect on the allocation of arrangement consideration.

Based on this analysis, the Company allocated $4,876,000 to the value of the license and recognized this amount as revenue in the year ended December 31, 2012 upon delivery as the risks and rewards associated with the License transferred at that time.

The remaining $124,000 of value was allocated based on the following:

• The estimated selling price of the Transition Services was approximately $600,000 resulting in consideration allocation of approximately $76,000. Repligen was able to derive a price for these services, in part because they are similar to services provided by a contract research organization. The selling price of the Transition Services was based on the Company’s internal FTE costs and external costs that it expects to incur to transition the program to Pfizer. The Company applied a mark-up on the internal FTE costs consistent with that of contract research organizations.

• The estimated selling price of the completion of the second cohort of the clinical trial was approximately $275,000 resulting in consideration allocation of approximately $35,000. This estimated selling price is based on the estimated, remaining costs to complete this cohort. Since the costs are pursuant to an arrangement negotiated with a third-party (the clinical site), the Company believes that the external cost estimate included in the agreement represents the best estimate of selling price for this unit of accounting.

• The estimated selling price of the Clinical Trial Material was approximately $105,000 resulting in consideration allocation of approximately $13,000. The estimated selling price is based upon the cost of procuring such material from the contract manufacturing organization that made the material. Since these costs were incurred pursuant to an arrangement negotiated with a third-party (the contract manufacturing organization), the Company believes that the costs included in the agreement represents the best estimate of selling price for this unit of accounting.

The Company intends to recognize the revenues related to the transfer of Clinical Trial Material upon transfer of title and risk of loss to Pfizer. The Company expects to recognize revenues related to the Transition Services and the completion of the second cohort ratably over the first six months of 2013.

In addition to the $5 million up-front payment, the Company is also eligible to receive $65 million in potential milestone payments comprised of: (i) up to $30 million related to the achievement of specified clinical milestone events; and (ii) up to $35 million related to the achievement of specified commercial sales events, specifically first commercial sale in specific territories. The Company may receive all, or a portion of, the first clinical milestone of $2 million in 2013 depending upon the development path chosen by Pfizer. If the Company receives a portion of this milestone, it expects to receive the balance of it by the end 2014.

Any future royalty payments, under the License Agreement will be recognized as revenue when they are earned.

The Scripps Research Institute

On April 6, 2007, the Company entered into an exclusive worldwide commercial license agreement (“Scripps License Agreement”) with The Scripps Research Institute (“Scripps”). Pursuant to the License Agreement, the Company obtained a license to use, commercialize and sublicense certain patented technology and improvements thereon, owned or licensed by Scripps, relating to compounds that may have utility in treating Friedreich’s ataxia, an inherited neurodegenerative disease. Research in tissues derived from patients, as well as from mice, indicates that the licensed compounds increase production of the protein frataxin, which suggests potential utility of these compounds in slowing or stopping progression of the disease. There are currently no approved treatments for Friedreich’s ataxia in the U.S.

Pursuant to the Scripps License Agreement, the Company agreed to pay Scripps an initial license fee of $300,000, certain royalty and sublicense fees and, in the event that the Company achieves specified developmental and commercial milestones, certain additional milestone payments. Total future milestone payments, if all milestones were achieved, would be approximately $4,300,000. In addition, the Company issued Scripps and certain of its designees 87,464 shares of the Company’s common stock, which had a value of $300,000 on the date of issuance.

In connection with the Scripps License Agreement, the Company issued warrants to an individual at Scripps to purchase up to 150,000 shares of common stock. The warrants have a seven-year term and are exercisable based on performance criteria as detailed in the warrant agreement governing such warrants. No expense has been recorded related to these warrants through December 31, 2012, as none of the performance criteria have been achieved. At this time, the Company does not believe that the performance criteria are probable of being achieved.

The Scripps License Agreement with Scripps expires or may be terminated (i) when all of the royalty obligations under the License Agreement expire; (ii) at any time by mutual written consent; (iii) by Scripps if the Company (a) fails to make payments under the License Agreement, (b) fails to achieve certain developmental and commercial objectives, (c) becomes insolvent, (d) is convicted of a felony relating to the manufacture, use or sale of the licensed technology, or (e) defaults in its performance under the License Agreement; or (iv) by the Company upon 90 days written notice.

Families of Spinal Muscular Atrophy

On October 22, 2009, the Company entered into an exclusive worldwide commercial license agreement (“FSMA License Agreement”) with Families of Spinal Muscular Atrophy (“FSMA”). Pursuant to the FSMA License Agreement, the Company obtained an exclusive license to develop and commercialize certain patented technology, and improvements thereon, owned or licensed by FSMA, relating to compounds that may have utility in treating spinal muscular atrophy (“SMA”). SMA is an inherited neurodegenerative disease in which a defect in the survival motor neuron gene (“SMN”) results in low levels of the protein SMN and leads to progressive damage to motor neurons, loss of muscle function and, in many patients, early death.

Pursuant to the FSMA License Agreement, the Company paid FSMA an initial license fee of $500,000 and a related sublicense fee of $175,000 in the year ended March 31, 2010. In April 2011, the Company paid an additional $500,000 milestone payment to FSMA. These license fees were recorded as research and development expense in the statements of operations. If all milestones are achieved, total financial obligations under this agreement, including milestone payments, sublicense fees, and other charges, could total approximately $16,000,000. Given the uncertain nature of such a development program, the likelihood that products or services will result from the research program is not known at this time. The Company has therefore ascribed no value to the license or the related liability.

The License Agreement with FSMA expires or may be terminated (i) on the later of: (a) when all related patents have expired or been abandoned, or (b) 10 years following the first commercial sale of a licensed product; (ii) by FSMA if the Company (a) fails to make payments under the License Agreement, (b) fails to use commercially reasonable efforts towards development and commercial objectives, (c) fails to maintain the required insurance or becomes insolvent, or (d) defaults in its performance under the License Agreement.

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Consolidated Statements of Operations Information for Each of Previous Eight Quarters (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Dec. 31, 2011	Mar. 31, 2011
Revenue:
Product revenue	$ 9,710,000	$ 11,123,000	$ 11,659,000	$ 9,342,000	$ 3,114,000	$ 5,742,000	$ 4,359,000	$ 3,150,000	$ 13,215,053	$ 11,810,869	$ 41,834,188		$ 14,961,397
Royalty and other revenue	9,104,000	3,981,000	3,865,000	3,482,000	4,051,000	2,889,000	3,295,000	2,756,000	10,235,194	9,573,770	20,432,348		12,329,627
Total revenue	18,814,000	15,104,000	15,524,000	12,824,000	7,165,000	8,631,000	7,654,000	5,906,000	23,450,247	21,384,639	62,266,536		27,291,024
Operating expenses:
Cost of product revenue	5,920,000	6,419,000	7,345,000	5,273,000	1,511,000	2,093,000	1,553,000	1,393,000	5,157,135	4,186,670	24,957,243		5,579,759
Cost of royalty and other revenue	620,000	594,000	537,000	462,000	481,000	418,000	416,000	376,000	1,315,315	1,160,775	2,213,004		1,537,666
Research and development	2,343,000	2,433,000	2,906,000	2,808,000	2,870,000	3,075,000	3,517,000	3,785,000	9,461,960	8,744,548	10,489,811		12,528,819
Selling, general and administrative	3,253,000	3,126,000	3,418,000	3,428,000	4,268,000	2,493,000	2,289,000	2,438,000	9,050,382	5,580,215	13,226,732		8,018,851
Contingent consideration - fair value adjustments	267,000	344,000			(427,000)						610,877
Gain on bargain purchase				(314,000)	(427,000)				(427,478)		(314,244)
Total operating expenses	12,403,000	12,916,000	14,206,000	11,657,000	8,703,000	8,079,000	7,775,000	7,992,000	24,557,314	19,672,208	51,183,423		27,665,095
Income (loss) from operations	6,411,000	2,188,000	1,318,000	1,167,000	(1,538,000)	552,000	(121,000)	(2,086,000)	(1,107,067)	1,712,431	11,083,113		(374,071)
Investment income	62,000	95,000	29,000	31,000	43,000	53,000	66,000	69,000
Interest expense	(14,000)	7,000	(27,000)	(22,000)	(28,000)			(13,000)	(27,773)	(12,683)	(56,714)		(26,167)
Other income (expense)	(41,000)	(500,000)	458,000	109,000	(623,000)				(623,094)		26,403
Income (loss) before income taxes	6,418,000	1,790,000	1,778,000	1,285,000	(2,146,000)	605,000	(55,000)	(2,030,000)	(1,596,881)	1,987,178	11,271,406	(1,596,881)	(43,509)
Income tax provision (benefit)	(3,135,000)	(16,000)	208,000	59,000	16,000				15,744		(2,884,631)	15,774
Net income (loss)	$ 9,553,000	$ 1,806,000	$ 1,570,000	$ 1,226,000	$ (2,162,000)	$ 605,000	$ (55,000)	$ (2,030,000)	$ (1,612,625)	$ 1,987,178	$ 14,156,037		$ (43,509)
Earnings (loss) per share:
Basic	$ 0.31	$ 0.06	$ 0.05	$ 0.04	$ (0.07)	$ 0.02	$ 0.00	$ (0.06)	$ (0.05)	$ 0.06	$ 0.46		$ 0.00
Diluted	$ 0.30	$ 0.06	$ 0.05	$ 0.04	$ (0.07)	$ 0.02	$ 0.00	$ (0.06)	$ (0.05)	$ 0.06	$ 0.45		$ 0.00
Weighted average shares outstanding:
Basic	31,132,000	30,948,000	30,845,000	30,730,000	30,715,000	30,797,000	30,812,000	30,782,000	30,774,467	30,778,430	30,914,424		30,781,881
Diluted	31,600,000	31,256,000	31,149,000	31,010,000	30,715,000	30,934,000	30,812,000	30,782,000	30,774,467	30,949,264	31,253,434		30,781,881

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Summary of Allocation of Consideration transferred (Detail) (Bio Flash Partners Limited Liability Company, USD $)	Dec. 31, 2012
Bio Flash Partners Limited Liability Company
Business Acquisition [Line Items]
Intangible assets subject to amortization	$ 1,430,000
Goodwill	994,000
Equipment	216,000
Total	$ 2,640,000

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Estimated Useful Life of Assets (Detail)	12 Months Ended
	Dec. 31, 2012
Leasehold improvements
Property, Plant and Equipment [Line Items]
Estimated Useful Life	Shorter of the term of the lease or estimated useful life
Equipment | Minimum
Property, Plant and Equipment [Line Items]
Estimated Useful Life	3 years
Equipment | Maximum
Property, Plant and Equipment [Line Items]
Estimated Useful Life	8 years
Furniture and fixtures
Property, Plant and Equipment [Line Items]
Estimated Useful Life	3 years

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Summary of Information Regarding Option Activity (Detail) (USD $)	12 Months Ended
	Dec. 31, 2012		Dec. 31, 2010
Options Outstanding
Options outstanding at December 31, 2011	2,823,400		2,566,450
Granted	368,690
Exercised	(609,400)
Forfeited/cancelled	(267,600)
Options outstanding at December 31, 2012	2,315,090		2,566,450
Options exercisable at December 31, 2012	1,447,600
Vested and expected to vest at December 31, 2012	2,186,609	[1]
Weighted average exercise price per share
Options outstanding at December 31, 2011	$ 4.05		$ 4.08
Granted	$ 3.65
Exercised	$ 3.06
Forfeited/cancelled	$ 4.44
Options outstanding at December 31, 2012	$ 4.20		$ 4.08
Options exercisable at December 31, 2012	$ 4.39
Vested and expected to vest at December 31, 2012	$ 4.21	[1]
Weighted average remaining contractual term (in years)
Options outstanding at December 31, 2012	6 years 1 month 28 days
Options exercisable at December 31, 2012	4 years 11 months 16 days
Vested and expected to vest at December 31, 2012	6 years 18 days	[1]
Aggregate intrinsic value
Options outstanding at December 31, 2012	$ 4,854,412
Options exercisable at December 31, 2012	2,783,183
Vested and expected to vest at December 31, 2012	$ 4,570,615	[1]

[1] This represents the number of vested options as of December 31, 2012 plus the number of unvested options expected to vest as of December 31, 2012 based on the unvested outstanding options at December 31, 2012 adjusted for estimated forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees.

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Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Income from Operations Before Income Taxes

Income tax data for the year ended December 31, 2012, the nine months ended December 31, 2011 and the year ended March 31, 2011:

	December 31, 2012		December 31, 2011			March 31, 2011
The components of income from operations before income taxes are as follows:
Domestic	$	11,175,638	$	(1,845,024	)	$	(43,509	)
Foreign		95,768		248,143			—
Total	$	11,271,406	$	(1,596,881	)	$	(43,509	)

Provision for Income Taxes

	December 31, 2012			December 31, 2011			March 31, 2011
The components of income from operations before income taxes are as follows:
Domestic	$	11,175,638		$	(1,845,024	)	$	(43,509	)
Foreign		95,768			248,143			—
Total	$	11,271,406		$	(1,596,881	)	$	(43,509	)
The current and deferred components of the provision for income taxes on operations are as follows:
Current	$	312,630		$	—		$	—
Deferred		(3,197,261	)		15,774			—
Total	$	(2,884,631	)	$	15,774		$	—
The jurisdictional components of the provision for income taxes on operations are as follows:
Federal	$	(2,915,673	)	$	48,000		$	—
State		115,307			—			—
Foreign		(84,265	)		(32,226	)		—
Total	$	(2,884,631	)	$	15,774		$	—

Consolidated Deferred Tax Assets or Liabilities

The Company’s consolidated deferred tax assets (liabilities) consist of the following:

	December 31, 2012			December 31, 2011
Deferred tax assets:
Temporary timing differences	$	4,152,000		$	4,277,000
Net operating loss carryforwards		15,041,000			20,065,000
Tax business credits carryforwards		2,160,000			4,166,000
Total deferred tax assets		21,353,000			28,508,000
Valuation allowance		(18,307,000	)		(28,476,000	)
Net deferred tax assets	$	3,046,000		$	32,000
Deferred tax liabilities:
Goodwill	$	(72,000	)	$	(48,000	)
Acquired intangibles		—			(89,000	)
Net deferred tax assets (liabilities)	$	2,974,000		$	(105,000	)

Reconciliation of Federal Statutory Rate to Effective Income Tax Rate

The reconciliation of the federal statutory rate to the effective income tax rate for the year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011 and the fiscal year ended March 31, 2011 is as follows:

	Period Ended,
	December 31, 2012					December 31, 2011					March 31, 2011
Income (loss) before income taxes	$	11,271,406			%	$	(1,596,881	)		%	$	(43,509	)		%
Expected tax (recovery) at statutory rate		3,944,996		35.0	%		(542,939	)	(34.0	)%		(14,793	)	(34.0	)%
Adjustments due to:
Difference between U.S. and foreign tax		(8,332	)	(0.1	)%		(19,287	)	(1.2	)%		—		(0.0	)%
State income and franchise taxes		357,866		3.2	%		52,905		3.3	%		96,141		221.0	%
Business tax credits		(67,276	)	(0.6	)%		(68,926	)	(4.3	)%		(66,126	)	(152.0	)%
Transaction costs		—		0.0	%		240,842		15.1	%		—		0.0	%
Gain on bargain purchase		(82,422	)	(0.7	)%		(112,427	)	(7.0	)%		—		(0.0	)%
Permanent differences		242,629		2.1	%		218,989		13.7	%		250,483		575.7	%
Change in valuation allowance		(7,272,092	)	(64.5	)%		246,587		15.4	%		(265,706	)	(610.7	)%
Provision (benefit) for income taxes	$	(2,884,631	)	(25.6	)%	$	15,744		1.0	%	$	—		(0.0	)%

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Acquisitions (Tables)

12 Months Ended

Dec. 31, 2012

Total Consideration Transferred

The total consideration transferred follows:

Cash consideration	$	26,445,000
Estimated fair value of contingent consideration		1,611,000
Total consideration transferred	$	28,056,000

Novozymes Biopharma Sweden Ab

Summary of Allocation of Consideration Transferred

The following chart summarizes the allocation of the fair value of assets acquired and liabilities assumed:

Accounts receivable	$	5,088,000
Inventory		10,497,000
Prepaid expenses		180,000
Fixed assets		9,089,000
Customer relationships and acquired technology		6,705,000
Deferred tax liability		(198,000	)
Accounts payable and other liabilities assumed		(2,563,000	)
Net assets acquired	$	28,798,000
Less total consideration transferred		(28,056,000	)
Gain on bargain purchase	$	742,000

Bio Flash Partners Limited Liability Company

Summary of Allocation of Consideration Transferred

The following chart summarizes the allocation of consideration transferred:

Intangible assets subject to amortization	$	1,430,000
Goodwill		994,000
Equipment		216,000
Total	$	2,640,000

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Stock-Based Compensation Expense (Detail) (USD $)	9 Months Ended		12 Months Ended
	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Stock-based compensation expense	$ 730,000	$ 748,000	$ 1,024,000	$ 1,003,000
Cost of product revenue
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Stock-based compensation expense	35,000	38,000	45,000	48,000
Research and development
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Stock-based compensation expense	191,000	164,000	219,000	226,000
Selling, general and administrative
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Stock-based compensation expense	$ 504,000	$ 546,000	$ 760,000	$ 729,000

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Intangible Assets (Detail) (USD $)	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 8,565,112	$ 8,161,711
Accumulated Amortization	(1,383,100)	(366,472)
Weighted Average Useful Life (in years)	8 years	8 years
Technology - developed
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	1,452,729	1,413,564
Accumulated Amortization	(360,748)	(184,402)
Weighted Average Useful Life (in years)	8 years	8 years
Patents
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	240,000	240,000
Accumulated Amortization	(87,500)	(57,500)
Weighted Average Useful Life (in years)	8 years	8 years
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	6,872,383	6,508,147
Accumulated Amortization	$ (934,852)	$ (124,570)
Weighted Average Useful Life (in years)	8 years	8 years

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CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (USD $)	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income	Accumulated Deficit
Beginning Balance at Mar. 31, 2010	$ 66,120,376	$ 307,618	$ 183,733,863		$ (117,921,105)
Beginning Balance (in shares) at Mar. 31, 2010		30,761,807
Net income (loss)	(43,509)				(43,509)
Share-based compensation expense	1,003,266		1,003,266
Exercise of stock options (in shares)		50,450
Exercise of stock options	6,571	505	6,066
Ending Balance at Mar. 31, 2011	67,086,704	308,123	184,743,195		(117,964,614)
Ending Balance (in shares) at Mar. 31, 2011		30,812,257
Net income (loss)	(1,612,625)				(1,612,625)
Unrealized gain on investments	6,338			6,338
Foreign currency translation adjustment	107,289			107,289
Share-based compensation expense	730,136		730,136
Repurchase and retirement of treasury stock (in shares)		(100,000)
Repurchase and retirement of treasury stock	(330,867)	(1,000)	(600,492)		270,625
Exercise of stock options (in shares)		2,500
Exercise of stock options	25	25
Ending Balance at Dec. 31, 2011	65,987,000	307,148	184,872,839	113,627	(119,306,614)
Ending Balance (in shares) at Dec. 31, 2011		30,714,757
Net income (loss)	14,156,037				14,156,037
Unrealized gain on investments	7,792			7,792
Foreign currency translation adjustment	1,790,551			1,790,551
Share-based compensation expense	1,024,152		1,024,152
Exercise of stock options (in shares)	609,400	480,284
Exercise of stock options	1,159,064	4,802	1,154,262
Ending Balance at Dec. 31, 2012	$ 84,124,596	$ 311,950	$ 187,051,253	$ 1,911,970	$ (105,150,577)
Ending Balance (in shares) at Dec. 31, 2012		31,195,041

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Stockholders' Equity

12 Months Ended

Dec. 31, 2012

Stockholders' Equity

4. Stockholders’ Equity

Common Stock and Warrants

At December 31, 2012, the Company has reserved 3,893,210 shares of common stock pursuant to the Plans, as described below. On April 6, 2007, the Company issued warrants to an individual at Scripps to purchase up to 150,000 shares of common stock at $0.01 per share, as discussed in Note 11. The warrants have a seven-year term and are exercisable based on performance criteria as detailed in the warrant agreement. At this time, the Company does not believe that the performance criteria are probable of being achieved in the near future.

Stock-Based Compensation

The Company recorded stock-based compensation expense of approximately $1,024,000 for the year ended December 31, 2012 for share-based awards granted under the Second Amended and Restated 2001 Repligen Corporation Stock Plan (the “2001 Plan”) and the Repligen Corporation 2012 Stock Option and Incentive Plan (the “2012 Plan,” and collectively with the 2001 Plan and the 1992 Repligen Corporation Stock Option Plan, the “Plans”). We recorded stock-based compensation expense of approximately $730,000 for the nine-month fiscal year ended December 31, 2011, and $748,000 for the nine-month period ended December 31, 2010 for share-based awards granted under the Plans. For the fiscal year ended March 31, 2011, we recorded stock-based compensation expense of approximately $1,003,000 for stock options granted under the 2001 Plan.

The following table presents stock-based compensation expense in the Company’s consolidated statements of operations:

	Year ended December 31, 2012		Nine Months ended December 31,				Year ended March 31, 2011
			2011		2010 (unaudited)
Cost of product revenue	$	45,000	$	35,000	$	38,000	$	48,000
Research and development		219,000		191,000		164,000		226,000
Selling, general and administrative		760,000		504,000		546,000		729,000
Total	$	1,024,000	$	730,000	$	748,000	$	1,003,000

The 2012 Plan allows for the granting of incentive and nonqualified options to purchase shares of common stock, restricted stock and other equity awards. Incentive options granted to employees under the Plans generally vest over a four to five-year period, with 20%-25% vesting on the first anniversary of the date of grant and the remainder vesting in equal yearly installments thereafter. Nonqualified options issued to non-employee directors and consultants under the Plans generally vest over one year. Options granted under the Plans have a maximum term of ten years from the date of grant and generally, the exercise price of the stock options equals the fair market value of the Company’s common stock on the date of grant. At December 31, 2012, options to purchase 2,315,090 shares were outstanding under the Plans. At December 31, 2012, 1,578,120 shares were available for future grant under the 2012 Plan.

The Company uses the Black-Scholes option pricing model to calculate the fair value of share-based awards on the grant date. The fair value of share-based awards granted during the year ended December 31, 2012, the nine-month fiscal year ended December 31, 2011, the nine-month period ended December 31, 2010 and the fiscal year ended March 31, 2011 were calculated using the following estimated assumptions:

	Year ended December 31,	Nine Months ended December 31,		Years ended March 31,
	2012	2011	2010	2011
Expected term (years)	6.5	6.5	6.5	6.5
Volatility	49.76% - 53.54%	53.09% - 55.76%	57.58% - 63.60%	55.94% - 63.60%
Risk-free interest rate	0.89% - 1.06%	1.25% - 2.38%	1.81% - 2.62%	1.81% - 2.83%
Expected dividend yield	—	—	—	—

Information regarding option activity for the year ended December 31, 2012 under the Plans is summarized below:

	Options Outstanding			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term (in years)		Aggregate Intrinsic Value
Options outstanding at December 31, 2011		2,823,400		$	4.05
Granted		368,690			3.65
Exercised		(609,400	)		3.06
Forfeited/cancelled		(267,600	)		4.44
Options outstanding at December 31, 2012		2,315,090		$	4.20		6.16	$	4,854,412
Options exercisable at December 31, 2012		1,447,600		$	4.39		4.96	$	2,783,183
Vested and expected to vest at December 31, 2012 (1)		2,186,609		$	4.21		6.05	$	4,570,615

(1) This represents the number of vested options as of December 31, 2012 plus the number of unvested options expected to vest as of December 31, 2012 based on the unvested outstanding options at December 31, 2012 adjusted for estimated forfeiture rates of 8% for awards granted to non-executive level employees and 3% for awards granted to executive level employees.

The aggregate intrinsic value in the table above represents the total pre-tax intrinsic value (the difference between the closing price of the common stock on December 31, 2012 of $6.28 per share and the exercise price of each in-the-money option) that would have been received by the option holders had all option holders exercised their options on December 31, 2012. The aggregate intrinsic value of stock options exercised during the year ended December 31, 2012 was approximately $1,384,000. The aggregate intrinsic value of stock options exercised during the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010 was approximately $8,000 and $43,000, respectively. The aggregate intrinsic value of stock options exercised during the fiscal year ended March 31, 2011 was approximately $76,000.

The weighted average grant date fair value of options granted during the year ended December 31, 2012 was $3.62. The weighted average grant date fair value of options granted during the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010 was $1.89 and $1.95, respectively. The weighted average grant date fair value of options granted during the fiscal year ended March 31, 2011 was $2.11. The total fair value of stock options that vested during the year ended December 31, 2012 was approximately $931,000. The total fair value of stock options that vested during the nine-month fiscal year ended December 31, 2011 and the nine-month period ended December 31, 2010 was approximately $804,000 and $817,000, respectively. The total fair value of stock options that vested during the fiscal year ended March 31, 2011 was approximately $993,000.

As of December 31, 2012, there was $1,605,995 of total unrecognized compensation cost related to unvested share-based awards. This cost is expected to be recognized over a weighted average remaining requisite service period of 2.76 years. We expect 739,009 unvested options to vest over the next five years.

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Royalty Arrangement with Bristol Myers Squibb Company - Additional Information (Detail) (USD $)	3 Months Ended								9 Months Ended		12 Months Ended		9 Months Ended		12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2012	Mar. 31, 2011	Dec. 31, 2011 Bristol Myers Squibb Company	Dec. 31, 2010 Bristol Myers Squibb Company	Dec. 31, 2012 Bristol Myers Squibb Company	Mar. 31, 2011 Bristol Myers Squibb Company	Mar. 31, 2008 Bristol Myers Squibb Company First $500 million of annual net sales	Mar. 31, 2008 Bristol Myers Squibb Company Next $500 million of annual net sales	Mar. 31, 2008 Bristol Myers Squibb Company Annual net sales in excess of $1 billion for each year from January 1, 2008 until December 31, 2013
Legal Settlement By Party [Line Items]
Bristol Settlement agreement, royalty payment rate																	1.80%	2.00%	4.00%
Annual net sales																	$ 500,000,000	$ 500,000,000	$ 1,000,000,000
Royalty revenue recognized	9,104,000	3,981,000	3,865,000	3,482,000	4,051,000	2,889,000	3,295,000	2,756,000	10,235,194	9,573,770	20,432,348	12,329,627	8,769,000	7,739,000	14,753,000	10,251,000
Percentage royalty revenue paid to University of Michigan															15.00%
Royalty expense													$ 1,315,000	$ 1,161,000	$ 2,213,000	$ 1,537,000

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Selected Quarterly Financial Data (Unaudited) (Tables)

12 Months Ended

Dec. 31, 2012

Consolidated Statements of Operations Information for Each of Previous Eight Quarters

The following table contains consolidated statements of operations information for each of the previous eight quarters. The Company believes that the following information reflects all normal recurring adjustments necessary for a fair presentation of the information for the periods presented. The operating results for any quarter are not necessarily indicative of results for any future period.

	December 31, 2012			September 30, 2012			June 30, 2012			March 31, 2012			December 31, 2011			September 30, 2011		June 30, 2011			March 31, 2011
	(in thousands, except per share amounts)
Revenue:
Product revenue	$	9,710		$	11,123		$	11,659		$	9,342		$	3,114		$	5,742	$	4,359		$	3,150
Royalty and other revenue		9,104			3,981			3,865			3,482			4,051			2,889		3,295			2,756
Total revenue		18,814			15,104			15,524			12,824			7,165			8,631		7,654			5,906
Operating expenses:
Cost of product revenue		5,920			6,419			7,345			5,273			1,511			2,093		1,553			1,393
Cost of royalty and other revenue		620			594			537			462			481			418		416			376
Research and development		2,343			2,433			2,906			2,808			2,870			3,075		3,517			3,785
Selling, general and administrative		3,253			3,126			3,418			3,428			4,268			2,493		2,289			2,438
Contingent consideration – fair value adjustments		267			344			—			—			(427	)		—		—			—
Gain on bargain purchase		—			—			—			(314	)		(427	)		—		—			—
Total operating expenses		12,403			12,916			14,206			11,657			8,703			8,079		7,775			7,992
Income (loss) from operations		6,411			2,188			1,318			1,167			(1,538	)		552		(121	)		(2,086	)
Investment income		62			95			29			31			43			53		66			69
Interest expense		(14	)		7			(27	)		(22	)		(28	)		—		—			(13	)
Other income (expense)		(41	)		(500	)		458			109			(623	)		—		—			—
Income (loss) before income taxes		6,418			1,790			1,778			1,285			(2,146	)		605		(55	)		(2,030	)
Income tax provision (benefit)		(3,135	)		(16	)		208			59			16			—		—			—
Net income (loss)	$	9,553		$	1,806		$	1,570		$	1,226		$	(2,162	)	$	605	$	(55	)	$	(2,030	)
Earnings (loss) per share:
Basic	$	0.31		$	0.06		$	0.05		$	0.04		$	(0.07	)	$	0.02	$	(0.00	)	$	(0.06	)
Diluted	$	0.30		$	0.06		$	0.05		$	0.04		$	(0.07	)	$	0.02	$	(0.00	)	$	(0.06	)
Weighted average shares outstanding:
Basic		31,132			30,948			30,845			30,730			30,715			30,797		30,812			30,782
Diluted		31,600			31,256			31,149			31,010			30,715			30,934		30,812			30,782

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Long Lived Assets by Geographic Area (Detail) (USD $)	Dec. 31, 2012	Dec. 31, 2011
Segment Reporting, Asset Reconciling Item [Line Items]
Long Lived Assets	$ 30,800,712	$ 29,162,008
United States
Segment Reporting, Asset Reconciling Item [Line Items]
Long Lived Assets	16,537,804	13,380,836
Sweden
Segment Reporting, Asset Reconciling Item [Line Items]
Long Lived Assets	$ 14,262,908	$ 15,781,172

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Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2012

Investments in Debt Securities

Investments in debt securities consisted of the following at December 31, 2012:

	December 31, 2012
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	2,000,897	$	353	$	(7	)	$	2,001,243
Corporate and other debt securities		8,835,098		8,854		—			8,843,952
		10,835,995		9,207		(7	)		10,845,195
Long-term marketable securities:
U.S. Government and agency securities		5,198,264		2,747		—			5,201,011
Corporate and other debt securities		4,711,679		3,525		(1,360	)		4,713,844
		9,909,943		6,272		(1,360	)		9,914,855
Total	$	20,745,938	$	15,479	$	(1,367	)	$	20,760,050

Investments in debt securities consisted of the following at December 31, 2011:

	December 31, 2011
	Amortized Cost		Gross Unrealized Gain		Gross Unrealized Loss			Fair Value
Marketable securities:
U.S. Government and agency securities	$	8,373,355	$	3,126	$	(233	)	$	8,376,248
Corporate and other debt securities		7,046,222		3,336		(4,370	)		7,045,188
		15,419,577		6,462		(4,603	)		15,421,436
Long-term marketable securities:
U.S. Government and agency securities		8,399,428		2,223		(91	)		8,401,560
Corporate and other debt securities		1,031,443		2,347		—			1,033,790
		9,430,871		4,570		(91	)		9,435,350
Total	$	24,850,448	$	11,032	$	(4,694	)	$	24,856,786

Contractual Maturities of Debt Securities

The contractual maturities of debt securities at December 31, 2012 were as follows:

	Amortized Cost		Fair Value
Due in 1 year or less	$	10,835,995	$	10,845,195
Due in 1 to 2 years		9,909,943		9,914,855
	$	20,745,938	$	20,760,050

Assets Measured at Fair Value on Recurring Basis

The following fair value hierarchy table presents information about each major category of the Company’s assets measured at fair value on a recurring basis as of December 31, 2012:

	Fair value measurement at reporting date using:
	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Total
Assets:
Money market funds	$	7,891,062	$	—	$	—	$	7,891,062
U.S. Government and agency securities		2,901,209		5,201,011		—		8,102,220
Corporate and other debt securities		—		13,557,796		—		13,557,796
Total	$	10,792,271	$	18,758,807	$	—	$	29,551,078

Roll Forward of Fair Value of Contingent Consideration

The following table provides a roll forward of the fair value of the contingent consideration:

Balance at December 31, 2011	$	2,197,226
Additions		—
Payments		(35,000	)
Changes in fair value		736,850
Balance at December 31, 2012	$	2,899,076

Schedule of Inventories

Inventories consist of the following:

	December 31, 2012		December 31, 2011
Raw Materials	$	4,064,317	$	3,563,395
Work-in-process		4,112,478		5,936,578
Finished products		2,966,900		3,863,100
Total	$	11,143,695	$	13,363,073

Estimated Useful Life of Assets

Depreciation is calculated using the straight-line method over the estimated useful life of the asset as follows:

Classification	Estimated Useful Life
Leasehold improvements	Shorter of the term of the lease or estimated useful life
Equipment	Three to eight years
Furniture and fixtures	Three years

Reconciliation of Basic and Diluted Shares Amounts

A reconciliation of basic and diluted share amounts is as follows:

	Year ended December 31,		Nine Months ended December 31,					Year ended March 31,
	2012		2011			2010		2011
Numerator:
Net income (loss)	$	14,156,037	$	(1,612,625	)	$	1,987,178	$	(43,509	)
Denominator:
Basic weighted average common shares outstanding		30,914,424		30,774,467			30,778,430		30,781,881
Weighted average common stock equivalents from assumed exercise of stock options and restricted stock awards		339,010		—			170,834		—
Diluted weighted average common shares outstanding		31,253,434		30,774,467			30,949,264		30,781,881
Basic net income (loss) per common share	$	0.46	$	(0.05	)	$	0.06	$	(0.00	)
Diluted net income (loss) per common share	$	0.45	$	(0.05	)	$	0.06	$	(0.00	)

Total Assets by Geographic Area

The following table represents the Company’s total assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	58,356,697	$	44,223,080
Sweden		38,653,466		31,833,734
Total	$	97,010,163	$	76,056,814

Long Lived Assets by Geographic Area

The following table represents the Company’s long-lived assets by geographic area:

	December 31, 2012		December 31, 2011
United States	$	16,537,804	$	13,380,836
Sweden		14,262,908		15,781,172
Total	$	30,800,712	$	29,162,008

Percentage of Revenue from Significant Customers

Revenue from significant customers as a percentage of the Company’s total revenue is as follows:

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
Orencia® Royalties from Bristol		24	%		37	%		37	%		38	%
Bioprocessing Customer A		42	%		44	%		45	%		42	%

Intangible assets

Intangible assets consisted of the following at December 31, 2012:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,452,729	$	(360,748	)		8
Patents		240,000		(87,500	)		8
Customer relationships		6,872,383		(934,852	)		8
Total intangible assets	$	8,565,112	$	(1,383,100	)		8

Intangible assets consisted of the following at December 31, 2011:

	Gross Carrying Amount		Accumulated Amortization			Weighted Average Useful Life (in years)
Technology – developed	$	1,413,564	$	(184,402	)		8
Patents		240,000		(57,500	)		8
Customer relationships		6,508,147		(124,570	)		8
Total intangible assets	$	8,161,711	$	(366,472	)		8

Total Revenue

Percentage by Geographic Area or Significant Customers

The following table represents the Company’s total revenue by geographic area (based on the location of the customer):

	Year ended December  31,			Nine Months ended December 31,						Year ended March  31,
	2012			2011			2010			2011
United States		46	%		48	%		48	%		50	%
Sweden		42	%		44	%		45	%		42	%
Other		12	%		8	%		7	%		8	%
Total		100	%		100	%		100	%		100	%

Accounts Receivable

Percentage by Geographic Area or Significant Customers

Significant accounts receivable balances as a percentage of the Company’s total trade accounts receivable and royalties and other receivable balances are as follows:

	December 31, 2012			December 31, 2011
Orencia® Royalties from Bristol		31	%		53	%
Bioprocessing Customer A		21	%		31	%
Pfizer		38	%		—