10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

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

For the quarterly period ended June 30, 2008

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 0-14656

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

(Former name, former address and former fiscal year, if changed since last report.)

Indicate by check mark 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 is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See 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	¨  (do not check if a smaller reporting company)	Smaller reporting company	¨

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

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of July 27, 2008.

Class	Number of Shares
Common Stock, par value $.01 per share	31,173,734

REPLIGEN CORPORATION

INDEX

		PAGE
	PART I. FINANCIAL INFORMATION
Item 1.	Unaudited Financial Statements
	Balance Sheets as of June 30, 2008 and March 31, 2008	3
	Statements of Operations for the Three-Month Periods Ended June 30, 2008 and 2007	4
	Statements of Cash Flows for the Three-Month Periods Ended June 30, 2008 and 2007	5
	Notes to Unaudited Financial Statements	6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	14
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	18
Item 4.	Controls and Procedures	18
	PART II. OTHER INFORMATION
Item 1.	Legal Proceedings	18
Item 1A.	Risk Factors	19
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	19
Item 3.	Defaults Upon Senior Securities	19
Item 4.	Submission of Matters to a Vote of Security Holders	19
Item 5.	Other Information	19
Item 6.	Exhibits	20
Signatures		21
Exhibit Index		22

2

REPLIGEN CORPORATION

BALANCE SHEETS

(Unaudited)

	June 30, 2008			March 31, 2008
ASSETS
Current assets:
Cash and cash equivalents	$	33,458,367		$	32,562,138
Marketable securities		14,931,652			17,221,653
Accounts receivable, less reserve of $ 10,000		2,399,233			1,125,801
Inventories		2,469,646			2,804,247
Prepaid expenses and other current assets		909,627			707,348
Total current assets		54,168,525			54,421,187
Property, plant and equipment, at cost:
Leasehold improvements		3,475,599			3,333,097
Equipment		3,452,696			3,271,446
Furniture and fixtures		232,631			226,655
		7,160,926			6,831,198
Less: Accumulated depreciation and amortization		(3,656,266	)		(3,417,941	)
		3,504,660			3,413,257
Long-term marketable securities		17,736,146			10,805,263
Restricted cash		200,000			200,000
TOTAL ASSETS	$	75,609,331		$	68,839,707
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	934,292		$	2,721,909
Accrued liabilities		1,757,735			1,867,900
Total current liabilities		2,692,027			4,589,809
Long-term liabilities		136,735			143,043
Total liabilities		2,828,762			4,732,852
Commitments and Contingencies
Stockholders’ equity:
Preferred stock, $.01 par value; authorized: 5,000,000 shares, issued or outstanding: none		—			—
Common stock, $.01 par value; authorized: 40,000,000 shares, issued and outstanding: 31,177,234 shares at June 30, 2008 and 31,072,934 shares at March 31, 2008		311,772			310,729
Additional paid-in capital		184,766,789			184,372,945
Accumulated deficit		(112,297,992	)		(120,576,819	)
Total stockholders’ equity		72,780,569			64,106,855
Total liabilities and stockholders’ equity	$	75,609,331		$	68,839,707

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

3

REPLIGEN CORPORATION

STATEMENTS OF OPERATIONS

(Unaudited)

	Three months ended June 30,
	2008			2007
Revenue:
Product revenue	$	5,693,343		$	5,731,476
Royalty and other revenue		7,966,902			247,342
Total revenue		13,660,245			5,978,818
Operating expenses: (1)
Cost of product revenue		1,846,401			1,714,299
Cost of royalty and other revenue		325,000			—
Research and development		2,084,125			2,137,326
Selling, general and administrative		1,446,571			2,142,131
Total operating expenses		5,702,097			5,993,756
Income (loss) from operations		7,958,148			(14,938	)
Investment income		532,585			257,367
Interest expense		(1,905	)		(2,451	)
Income before taxes		8,488,828			239,978
Income tax provision		210,000			—
Net income	$	8,278,828		$	239,978
Earnings per share:
Basic	$	.27		$	.01
Diluted	$	.26		$	.01
Weighted average shares outstanding:
Basic		31,152,556			30,564,494
Diluted		31,585,112			31,127,099
(1)    Includes non-cash stock-based compensation as follows:
Cost of product revenue	$	10,827		$	7,030
Research and development		31,676			55,066
Selling, general and administrative		117,929			124,478

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

4

REPLIGEN CORPORATION

STATEMENTS OF CASH FLOWS

(Unaudited)

	Three months ended June 30,
	2008			2007
Cash flows from operating activities:
Net income	$	8,278,828		$	239,978
Adjustments to reconcile net income to net cash provided by (used in) operating activities:
Issuance of common stock for license		—			300,000
Depreciation and amortization		241,325			189,158
Stock-based compensation expense		160,432			186,574
Changes in assets and liabilities:
Accounts receivable		(1,273,432	)		(1,545,522	)
Inventories		334,601			(116,623	)
Prepaid expenses and other current assets		(202,280	)		3,359
Accounts payable		(1,787,617	)		268,836
Accrued liabilities		(108,571	)		(274,578	)
Long-term liabilities		(6,308	)		(5,265	)
Net cash provided by (used in) operating activities		5,636,978			(754,083	)
Cash flows from investing activities:
Purchases of marketable securities		(10,540,882	)		(7,319,705	)
Redemptions of marketable securities		5,900,000			7,200,000
Purchases of property, plant and equipment		(332,727	)		(195,016	)
Net cash (used in) investing activities		(4,973,609	)		(314,721	)
Cash flows from financing activities:
Exercise of stock options		234,455			120,710
Principal payments under capital lease obligations		(1,595	)		(1,447	)
Net cash provided by financing activities		232,860			119,263
Net increase in cash and cash equivalents		896,229			(949,541	)
Cash and cash equivalents, beginning of period		32,562,138			7,726,505
Cash and cash equivalents, end of period	$	33,458,367		$	6,776,964
Supplemental disclosure of noncash activities:
Disposal of fully depreciated equipment	$	3,000		$	—

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

5

REPLIGEN CORPORATION

NOTES TO FINANCIAL STATEMENTS

(Unaudited)

1. Basis of Presentation

The financial statements included herein have been prepared by Repligen Corporation (the “Company”, “Repligen” or “we”) in accordance with accounting principles generally accepted in the United States and pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”), for quarterly reports on Form 10-Q and Article 10 of Regulation S-X and do not include all of the information and footnote disclosures required by accounting principles generally accepted in the United States. These financial statements should be read in conjunction with the audited financial statements and accompanying notes thereto included in our annual report on Form 10-K for the year ended March 31, 2008.

In the opinion of management, the accompanying unaudited financial statements include all adjustments, consisting of only normal, recurring adjustments necessary for a fair presentation of the financial position, results of operations and cash flows. The results of operations for the interim periods presented are not necessarily indicative of results to be expected for the entire year.

The preparation of financial statements in conformity with accounting principles generally accepted in the United States 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.

2. Revenue Recognition

The Company applies Staff Accounting Bulletin No. 104, “Revenue Recognition,” (“SAB 104”), and Emerging Issues Task Force 00-21, Revenue Arrangements with Multiple Deliverables (“EITF 00-21”) to all its revenue arrangements.

The Company generates product revenues from the sale of Protein A products to customers in the pharmaceutical and process chromatography industries and from the sale of SecreFlo^® to hospital-based gastroenterologists. In accordance with SAB 104, 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 are based on management’s judgments primarily regarding the fixed nature of the fee charged for product delivered, and the collectability of those fees. The Company has a few longstanding customers who comprise the majority of product revenue and have excellent payment history. The Company has had no significant write-offs of uncollectible invoices in the periods presented. Should changes in conditions cause management to determine that these criteria are not met for certain future transactions, revenue recognized for any reporting period could be adversely affected.

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 financial statements historically. Should changes in conditions cause management to determine that warranty, returns or other sale-related reserves are necessary for certain future transactions, revenue recognized for any reporting period could be adversely affected.

The Company also recognizes royalty revenue in the period earned. Royalty revenue for the period was predominantly generated pursuant to an agreement with Bristol-Myers Squibb Company (“Bristol”) entered into on April 7, 2008 (see Note 14). The Company also recognized $0.1 million from ChiRhoClin for their sales of secretin during the quarter. Bristol royalties are based on Bristol’s net U.S. sales of Orencia^® through 2013, are payable quarterly. During the three months ended June 30, 2008, the Company recognized $7.9 million in Bristol royalties, which included an initial $5.0 million payment, $1.3 million for sales of Orencia^® from January 1, 2008 to March 31, 2008, and $1.6 million for sales of Orencia^® from April 1, 2008 to June 30, 2008. Bristol began selling Orencia^® in February 2006. The initial $5.0 million payment was considered payment for sales from February 2006 to December 31, 2007 and is consistent with the royalty rate applied to sales of Orencia^® after December 31, 2007. This initial payment is non-refundable, there are no future delivery obligations on the part of the Company, and our rights to this revenue are not dependent on future sales of Orencia^®, if any. Therefore, the Company has recognized this initial payment as royalty revenue during the first quarter of fiscal 2009.

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Research revenue is recognized on a cost plus fixed-fee basis when the expense has been incurred and services have been performed. Determination of which costs incurred qualify for reimbursement under the terms of the contractual agreement and the timing of when such costs were incurred involves the judgment of management. The Company believes its calculations are consistent with the agreed-upon terms as stated in the arrangement. However, should the estimated calculations change or be challenged by our research partners, 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 this sponsored research and development project. During the three months ended June 30, 2007, the Company recognized $0.2 million in research revenue. No research revenue was earned in the three months ended June 30, 2008.

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

3. Earnings (Loss) Per Share

We follow the provisions of Statement of Financial Accounting Standard or SFAS No. 128, “Earnings Per Share,” (“SFAS 128”). Basic earnings per share for the three-month periods ended June 30, 2008 and 2007 were computed on the basis of the weighted average number of shares of common stock outstanding during the period. Diluted earnings per share is computed on the basis of the weighted average number of shares of common stock plus the effect of dilutive potential common shares outstanding during the period using the treasury stock method in accordance with SFAS 128. Dilutive potential common shares include outstanding stock options.

Basic and diluted weighted average shares outstanding were as follows:

	Three Months Ended June 30,
	2008	2007
Weighted average common shares	31,152,556	30,564,494
Dilutive common stock options	432,556	562,605
Weighted average common shares, assuming dilution	31,585,112	31,127,099

For the three-month periods ended June 30, 2008 and 2007, options to purchase 716,500 and 530,500 shares of our 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.

At June 30, 2008, there were outstanding options to purchase 1,889,950 shares of our common stock at a weighted average exercise price of $4.28 per share.

4. Stock-Based Compensation

The Company follows the fair value recognition provisions of SFAS No. 123R, Share-Based Payment—An Amendment of FASB Statements No. 123 and 95,” or SFAS No. 123R, using the modified prospective transition method.

For the three months ended June 30, 2008 and 2007, the Company recorded stock-based compensation expense of approximately $160,000 and $187,000, respectively, for stock options granted under the Amended and Restated 2001 Repligen Corporation Stock Plan.

The Plans allow for the granting of incentive and nonqualified options and restricted stock and other equity awards to purchase shares of Common Stock. 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 June 30, 2008, options to purchase 1,577,450 shares were outstanding under the Amended and Restated 2001 Repligen Corporation Plan and options to purchase 312,500 shares were outstanding under the 1992 Repligen Corporation Stock Option Plan. At June 30, 2008, 94,909 shares were available for future grant under the Amended and Restated 2001 Repligen Corporation Stock Plan.

The Company recognizes 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. SFAS No. 123R requires

7

forfeitures to be 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, the Company has calculated an 8% annual forfeiture rate for non-director level employees, a 3% annual forfeiture rate for director level employees, and a 0% forfeiture rate for non-employee members of the Board of Directors, which it believes 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 the Company’s current estimates, such amounts will be recorded as a cumulative adjustment in the period estimates are revised.

Information regarding option activity for the three months ended June 30, 2008 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 April 1, 2008	1,622,750		$	3.78
Granted	391,500		$	5.87
Exercised	(99,300	)	$	2.36
Forfeited/Cancelled	(25,000	)	$	5.95
Options outstanding at June 30, 2008	1,889,950		$	4.26	6.65	$	2,010,716
Options exercisable at June 30, 2008	1,033,600		$	3.90	4.59	$	1,482,739
Vested and expected to vest at June 30, 2008 (1)	1,826,439		$	4.26	6.64	$	1,914,746

(1) This represents the number of vested options as of June 30, 2008 plus the number of unvested options expected to vest as of June 30, 2008 based on the unvested outstanding options at June 30, 2008 adjusted for the estimated forfeiture rate of 8% for awards granted to non-director level employees and 3% for awards granted to director level employees as described above.

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 June 30, 2008 of $4.72 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 June 29, 2008.

The weighted average grant date fair value of options granted during the three months ended June 30, 2008 and 2007 was $3.70 and $2.61, respectively. The total fair value of stock options that vested during the three months ended June 30, 2008 and 2007 was approximately $261,230 and $316,420, respectively.

As of June 30, 2008, there was approximately $953,100 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 2.65 years. The Company expects approximately 793,000 in unvested options to vest over the next five years.

5. Cash, Cash Equivalents and Marketable Securities

We follow the provisions of SFAS No. 115, “Accounting for Certain Investments in Debt and Equity Securities.” At June 30, 2008, our investments included money market funds as well as short-term and long-term marketable securities, which are classified as held-to-maturity investments as we have the positive intent and ability to hold to maturity. As a result, these investments are recorded at amortized cost. Marketable securities are investments with original maturities of greater than 90 days. Long-term marketable securities are investment grade securities with maturities of greater than one year.

At March 31, 2008, marketable securities also included investment grade auction rate securities. Auction rate securities have long-term underlying maturities, but have interest rates that are reset every 90 days or less, at which time the securities can typically be purchased or sold. Auction rate securities were classified as available-for-sale and reported at fair value. Due to the reset feature and their carrying value equaling their fair value, there were no gross unrealized gains or losses from these short-term investments. As of June 30, 2008, the Company has sold all remaining auction rate securities without incurring any losses.

8

Cash, cash equivalents and marketable securities consist of the following:

	June 30, 2008		March 31, 2008
Cash and cash equivalents	$	33,458,367	$	32,562,138
Marketable securities:
Auction rate securities	$	—	$	900,000
Corporate and other debt securities		14,931,652		16,321,653
	$	14,931,652	$	17,221,653
Long-term marketable securities:
U.S. Government and agency securities	$	10,555,097	$	—
Corporate and other debt securities		7,181,049		10,805,263
	$	17,736,146	$	10,805,263

The average remaining maturity of long-term marketable securities at June 30, 2008 is approximately 17 months.

Restricted cash of $200,000 is related to our facility lease obligation.

6. Fair Value Measurement

In February 2007, the FASB issued SFAS No. 159, “The Fair Value Option for Financial Assets and Financial Liabilities — including an Amendment of FASB Statement No. 115” (“SFAS 159”), which allows an entity to choose to measure certain financial instruments and liabilities at fair value. Subsequent measurements for the financial instruments and liabilities an entity elects to fair value will be recognized in earnings. SFAS 159 also establishes additional disclosure requirements. SFAS 159 was effective for the Company beginning April 1, 2008. The adoption of SFAS 159 did not have a material impact on our condensed consolidated statement of financial position, results of operations and cash flows. We did not elect to remeasure any existing financial assets or liabilities under the provisions of SFAS 159.

In September 2006, the Financial Accounting Standards Board (FASB) issued Statement of Financial Accounting Standards (SFAS) No. 157, “Fair Value Measurements,” effective for financial statements issued for fiscal years beginning after November 15, 2007. SFAS No. 157 replaces multiple existing definitions of fair value with a single definition, establishes a consistent framework for measuring fair value and expands financial statement disclosures regarding fair value measurements. This Statement applies only to fair value measurements that already are required or permitted by other accounting standards and does not require any new fair value measurements. In February 2008, the FASB issued FASB Staff Position (FSP) No. 157-2, which delayed until January 1, 2009 the effective date of SFAS No. 157 for nonfinancial assets and liabilities that are not recognized or disclosed at fair value in the financial statements on a recurring basis.

The adoption of SFAS No. 157 for our financial assets and liabilities in the first quarter of fiscal 2009 did not have a material impact on our financial position or results of operations. Our nonfinancial assets and liabilities that meet the deferral criteria set forth in FSP No. 157-2 include property, plant and equipment. We do not expect that the adoption of SFAS No. 157 for these nonfinancial assets and liabilities will have a material impact on our financial position or results of operations.

In determining the fair value of its financial assets and liabilities, the Company uses various valuation approaches. SFAS 157 establishes 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

9

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 held-to-maturity securities, which are fixed income investments, are comprised of obligations of U.S. government agencies, corporate debt securities and other interest bearing securities. These held-to-maturity securities are recorded at amortized cost and are therefore not included in our market value measurement disclosure. Money market funds are valued using quoted market prices with no valuation adjustments applied. Accordingly, these securities are categorized in Level 1.

The following fair value hierarchy table presents information about each major category of the Company’s financial assets and liabilities measured at fair value on a recurring basis as of June 30, 2008:

	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)	Balance as of June 30, 2008
Assets:
Money market funds	24,452,354			24,452,354

There were no remeasurements to fair value during the three months ended June 30, 2008 of financial assets and liabilities that are not measured at fair value on a recurring basis.

7. Inventories

Inventories relate to the Company’s Protein A business. The Company values inventory at the lower of cost or market on a first-in, first-out basis. Cost includes material, labor and applicable manufacturing overhead costs. 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 goods. Expected sales volumes are determined based on supply forecasts provided by key customers for the next three to twelve months. The Company writes down inventory that has become obsolete, has a cost basis in excess of its expected net realizable value, or is in excess of expected requirements to cost of goods sold. Protein A finished goods are manufactured 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 financial statements, there have been no material adjustments related to a revised estimate of inventory valuations.

Inventories consist of the following:

	June 30, 2008		March 31, 2008
Raw materials	$	1,416,659	$	1,676,402
Work in process		898,717		676,769
Finished goods		154,270		451,076
	$	2,469,646	$	2,804,247

8. Accrued Expenses and Other Current Liabilities

The Company prepares its financial statements in accordance with accounting principles generally accepted in the United States. These principles require that the Company estimate accrued liabilities. This process involves identifying services performed on the Company’s behalf and estimating the level of service performed and the associated cost incurred for such service as of each balance sheet date. Examples of estimated accrued expenses include: 1) Fees paid to contract

10

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; 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 which 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 are often judgmental. The Company makes 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 has been no material adjustments to our accrued liabilities in any of the periods presented in the accompanying financial statements.

Accrued expenses and other current liabilities consist of the following:

	June 30, 2008		March 31, 2008
Employee compensation	$	418,221	$	621,982
Royalty and license fees		344,196		97,804
Research & development		182,421		201,825
Professional fees		164,889		451,287
Other accrued expenses		324,106		217,874
Other current liabilities		213,967		217,162
Unearned revenue		109,935		59,965
	$	1,757,735	$	1,867,899

9. Income Taxes

The Company had income before taxes of approximately $8,489,000 for the three months ended June 30, 2008. The Company had pretax income of approximately $240,000 for the three months ended June 30, 2007. The Company had no income tax provision for the three months ended June 30, 2007. The Company had an income tax provision of $210,000 for the three months ended June 30, 2008. For the three months ended June 30, 2008, the effective income tax rate was 2.47%. The effective income tax rate is based upon the estimated income for the year and the composition of the income in different jurisdictions. The effective tax rate differs from the statutory tax rate due to the utilization of prior year net operating losses and credits, offset by the effects of the alternative minimum tax on income derived during the fiscal year.

The Company has net operating loss carryforwards of approximately $63,517,000, business tax credits carryforwards of approximately $2,205,000, and other tax credits of approximately $733,000 available to reduce future federal income taxes, if any. Additionally, the Company also has business tax credits carryforwards of approximately $2,665,000 available to reduce future state income taxes, if any. The Company has utilized all available state net operating loss carryforwards. The net operating loss and business tax credits carryforwards will continue to expire at various dates through March 2026. 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.

As of June 30, 2008, a full valuation allowance has been provided against the net operating losses, business tax credits and other deferred tax assets, as it is uncertain if the Company will realize the benefits of such deferred tax assets.

10. Comprehensive Income/Loss

We follow the provisions of SFAS No. 130, “Reporting Comprehensive Income” (“SFAS 130”). SFAS 130 requires disclosure of all components of comprehensive income on an annual and interim basis. Comprehensive income is defined as the change in equity of a business enterprise during a period resulting from transactions and other events and circumstances from non-owner sources. Our comprehensive income is equal to our reported net income for all periods presented.

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11. Segment Reporting

We follow the provisions of SFAS No. 131, “Disclosures about Segments of an Enterprise and Related Information” (“SFAS 131”). SFAS 131 establishes standards for reporting information regarding operating segments in annual financial statements and requires selected information for those segments to be presented in interim financial reports issued to stockholders. SFAS 131 also establishes standards for related disclosures about products and services and geographic areas. The chief operating decision maker, or decision-making group, in making decisions regarding how to allocate resources and assess performance, identifies operating segments as components of an enterprise about which separate discrete financial information is available for evaluation. To date, we view our operations and manage our business as one operating segment. As a result, the financial information disclosed herein represents all of the material financial information related to our principal operating segment.

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

	Three months ended June 30,
	2008		2007
Sweden	33	%	67	%
US	64	%	29	%
Other	3	%	4	%
	100	%	100	%

Royalty revenue from Bristol represented 58% of the Company’s total revenue for the three months ended June 30, 2008. The Company’s two largest Protein A customers accounted for 33% and 2% of total revenues for the three months ended June 30, 2008 and 67% and 10% of revenues for the three months ended June 30, 2007.

At June 30, 2008, Bristol’s royalty payment comprised 65% of our accounts receivable. One of the Company’s largest Protein A customers accounted for 26% of our accounts receivable as of June 30, 2008. Two of the Company’s largest Protein A customers accounted for 20% and 24% of accounts receivable as of March 31, 2008, respectively.

12. New Accounting Pronouncements

In December 2007, the Financial Accounting Standards Board (“FASB”) issued SFAS No. 141(R), “Business Combinations” (“SFAS 141(R)”) and SFAS No. 160, “Accounting and Reporting of Noncontrolling Interests in Consolidated Financial Statements — an amendment of ARB No. 51” (“SFAS 160”). These standards will significantly change the accounting and reporting for business combination transactions and noncontrolling (minority) interests in financial statements, including capitalizing at the acquisition date the fair value of acquired in process research and development projects, and remeasuring and writing down these assets, if necessary, in subsequent periods during their development. The new standards will be applied prospectively for business combinations that occur for the Company on or after April 1, 2009, except that presentation and disclosure requirements of SFAS 160 regarding minority interests shall be applied retrospectively.

In December 2007, the FASB ratified EITF No. 07-1, “Accounting for Collaborative Agreements” (“EITF 07-1”). EITF 07-1 provides guidance regarding financial statement presentation and disclosure of collaborative arrangements, as defined, which includes arrangements the Company has entered into regarding development and commercialization of products. EITF 07-1 is effective for the Company as of April 1, 2009. The Company has not yet completed its evaluation of EITF 07-1, but does not currently believe that adoption will have a material impact on its results of operations, financial position or cash flows.

13. Scripps Agreements

License Agreement

On April 6, 2007 (the “Effective Date”), the Company entered into an exclusive worldwide commercial license agreement (“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 which may have utility in treating Friedreich’s Ataxia, an inherited neurodegenerative disease. Research in tissues derived from patients, as well as, in 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.

Pursuant to the License Agreement, the Company agreed to pay Scripps an initial license fee of $300,000, certain royalty and sublicense fees and, in the event the Company achieves specified developmental and commercial milestones, certain additional milestone payments. In addition, the Company issued Scripps 87,464 shares of the Company’s common stock (the “Shares”) representing $300,000 as of the Effective Date. The Company recorded the initial license payment and the value of the shares issued as research and development costs in the Company’s statement of operations in the first quarter of fiscal 2008.

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If the value of the Shares did not equal at least $300,000 on the one-year anniversary of the Effective Date, the Company would have had to make a cash payment to Scripps equal to the difference. At April 6, 2008, the one-year anniversary of the Effective Date, the fair value of the shares exceeded $300,000; therefore, no liability was recorded. Furthermore, the Company issued warrants to an individual at Scripps to purchase up to 150,000 shares of common stock. The warrants have a 7-year term and are exercisable based on performance criteria as detailed in the warrant agreement. No expense has been recorded related to these warrants in fiscal 2008 or for the three-month period ended June 30, 2008, 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 in the near future.

The 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.

Research Funding and Option Agreement

On October 26, 2007, the Company entered into a research funding and option agreement (“Funding Agreement”) with Scripps to fund a research program for the research and development of compounds that may have utility in the treatment of Friedreich’s Ataxia. Pursuant to the Funding Agreement, the Company is required to fund approximately $140,000 annually, payable quarterly, which are recorded as research and development expenses. In exchange for funding the research, Scripps will grant an exclusive option to the Company to acquire a sole, worldwide license, including the right to sublicense, manufacture and sell products, and services that result from the research program. There are no guaranties or warranties that products or services may result from the research program, and the Company has ascribed no value to the license.

The Funding Agreement expires or may be terminated (i) when all of the royalty obligations under the Funding Agreement expire; (ii) at any time by mutual written consent; (iii) by Scripps if the Company (a) fails to make payments under the Funding 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 Funding Agreement; or (iv) by the Company upon 90 days written notice.

14. Legal Proceedings

ImClone Systems

In May 2004, the Company and the Massachusetts Institute of Technology (“MIT”) filed an action in the United States District Court for the District of Massachusetts against ImClone Systems, Incorporated (“ImClone”) for infringement of U.S. Patent No. 4,663,281 (“the ‘281 patent”) based on ImClone’s manufacture and sale of Erbitux^®. The ‘281 patent, which covers the use of certain genetic elements that increase protein production in a mammalian cell, is assigned to MIT and exclusively licensed to Repligen.

On September 10, 2007, the Company and MIT entered into a settlement agreement (the “ImClone Settlement”) with ImClone relating to the lawsuit against ImClone for infringement of the ‘281 patent. Pursuant to the ImClone Settlement, ImClone made a payment of $65 million to Repligen and MIT that resulted in net proceeds to Repligen of $40.17 million, as follows:

Gross proceeds from ImClone Settlement agreement	$	65,000,000
Less: Amounts paid to MIT		(11,000,000	)
Less: Legal fees and other costs		(13,830,000	)
Net gain on litigation settlement	$	40,170,000

The ImClone Settlement served as the basis for the Company and MIT to dismiss the lawsuit against ImClone and for the Company to grant ImClone a non-exclusive sublicense to the ‘281 patent and certain other intellectual property. There are no further obligations to the Company with respect to the sublicenses. The net gain on litigation settlement was recorded as a separate component of operating expenses in the Company’s statement of operations in fiscal 2008.

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Bristol-Myers Squibb Company

In January 2006, Repligen and the University of Michigan jointly filed a complaint against Bristol in the United States District Court for the Eastern District of Texas for infringement of U.S. Patent No. 6,685,941 (“the ‘941 patent”) for the commercial sale of Orencia^®. The ‘941 patent, entitled “Methods of Treating Autoimmune Disease via CTLA4-Ig,” covers methods of using CTLA4-Ig to treat rheumatoid arthritis, as well as other therapeutic methods. Repligen has exclusive rights to this patent from its owners, the University of Michigan and the U.S. Navy. In February 2006, Bristol answered the complaint and counterclaimed seeking a declaratory judgment that the ‘941 patent is invalid and unenforceable and that Bristol does not infringe the patent.

On April 7, 2008, Repligen and the University of Michigan entered into a settlement agreement (the “Bristol Settlement”) with Bristol relating to the lawsuit against Bristol for infringement of the ‘941 patent. Pursuant to the Bristol Settlement, Bristol made an initial payment of $5 million to Repligen. The settlement further 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 agreement, the Company has recognized $7.9 million in royalty revenue in the three months ended June 30, 2008, which was comprised of the $5 million initial payment, $1.3 million for sales of Orencia^® from January 1, 2008 through March 31, 2008, and $1.6 million for sales of Orencia^® from April 1, 2008 through June 30, 2008 (see Note 2). The Bristol Settlement served as the basis for Repligen and the University of Michigan to dismiss the lawsuit against Bristol and for Repligen and the University of Michigan to grant to Bristol an exclusive worldwide license to the ‘941 patent and certain other intellectual property.

Repligen must also remit to the University of Michigan 15% of all royalty revenue received from Bristol, after first deducting certain legal and other costs incurred related to the settlement. The Company has incurred $5.7 million in such legal costs, which when deducted from the $7.9 million in royalty revenue earned during the quarter, results in a net amount due to the University of Michigan of $325,000. This operating expense has been included on our Statements of Operations under the line item “Cost of royalty and other revenue”.

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Overview

We are a biopharmaceutical company focused primarily on the development of novel therapeutics for diseases that affect the central nervous system. A number of drug development programs are currently being conducted to evaluate our drug candidates in diseases such as bipolar disorder and neurodegeneration. In addition, we sell Protein A for monoclonal antibody purification and receive royalties on intellectual property that we license to third parties. Our business strategy is to deploy the profits from our current commercial products and patents licensing revenues to enable us to invest in the development of our therapeutic product candidates while reducing our financial risk.

Critical Accounting Policies and Estimates

A “critical accounting policy” is one which is both important to the portrayal of the Company’s financial condition and results and requires management’s most difficult, subjective or complex judgments, often as a result of the need to make estimates about the effect of matters that are inherently uncertain. For additional information, please see the discussion of our significant accounting policies in Note 2 to the Financial Statements included in our Annual Report on Form 10-K dated March 31, 2008.

Results of Operations

Three months ended June 30, 2008 vs. June 30, 2007

Total revenue

Total revenues for the three-month periods ended June 30, 2008 and June 30, 2007 were approximately $13,660,000 and $5,979,000 respectively, an increase of $7,681,000 or 128%.

Sales of Protein A for the quarters ended June 30, 2008 and June 30, 2007 were $5,525,000 and $5,230,000, respectively. The increase of $295,000, or 6%, was largely the result of increased pricing, as volume remained consistent with the prior quarter. The Company sells different Protein A products at different price points. The mix of products sold varies and impacts the fluctuations in total sales revenue and cost of product revenues from quarter to quarter.

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Substantially all of our products based on recombinant Protein A 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, Crohn’s disease and a variety of cancers. Sales of Protein A are therefore impacted by the timing of large-scale production orders and on the regulatory approvals for such antibodies, which may result in significant quarterly fluctuations.

As previously announced, in April 2008, we settled our outstanding litigation with Bristol. We have therefore begun recognizing royalty revenue in the first quarter of fiscal year 2009 for Bristol’s ongoing sales of Orencia^® which is used in the treatment of rheumatoid arthritis. Pursuant to the Bristol Settlement, we have recognized $7,896,000 in royalty revenue in the three months ended June 30, 2008, which was comprised of the $5,000,000 initial payment as well as $1,330,000 and $1,566,000 for Bristol’s net U.S. sales of Orencia^® during the three months ended March 31, 2008 and June 30, 2008, respectively. Additionally, during the three-month periods ended June 30, 2008 and June 30, 2007, we earned and recognized approximately $110,000 and $47,000, respectively, in royalty revenue from ChiRhoClin.

Sales of SecreFlo^® for the quarter ended June 30, 2008 and June 30, 2007 were $168,000 and $501,000, respectively, which represents a decrease of $333,000 or 66%. The settlement in fiscal 2005 with ChiRhoClin, our sole supplier of SecreFlo^®, provided for a certain amount of vials of product that we can ultimately ship. The final shipment of SecreFlo^® to the Company from ChiRhoClin was received in fiscal 2008, and we expect to sell our remaining inventory by the end of the second quarter in fiscal 2009.

During the three-month period ended June 30, 2007, we recognized approximately $200,000 of revenue from a sponsored research and development project under an agreement with SMRI. This project reached its completion in fiscal 2008 and thus no revenue was recognized in the three-month period ended June 30, 2008. Research revenue is recognized for costs plus fixed-fee contracts as costs are incurred.

Costs and Operating expenses

Total costs and operating expenses were approximately $5,702,000 and $5,994,000 for the three-month periods ended June 30, 2008 and June 30, 2007, respectively, a decrease of $292,000 or 5%.

Cost of product revenue was approximately $1,846,000 and $1,714,000 for the three-month periods ended June 30, 2008 and June 30, 2007, respectively, an increase of $132,000 or 8%. This increase is primarily due to the 6% increase in Protein A sales noted above, as well as increased depreciation expenses related to expansion of our manufacturing capacity and increased headcount in the three-month period ended June 30, 2008.

In connection with the Bristol Settlement, we must remit 15% of royalty revenue received through the expiration of the settlement agreement in December 2013, after deducting certain allowable legal and other costs, to the University of Michigan. For the three-month period ended June 30, 2008, this cost of royalty revenue was $325,000.

Research and development expenses were approximately $2,084,000 and $2,137,000 for the three-month periods ended June 30, 2008 and June 30, 2007, respectively, a decrease of $53,000 or 2%. The decrease is largely due to $600,000 of licensing expenses from the prior year associated with the signing of the License Agreement with Scripps that did not recur in the current period, and lower spending in our uridine for bi-polar depression trials compared to the first quarter of fiscal 2008. These decreases were offset by $473,000 of internal and third party clinical research costs incurred upon the commencement of our Phase 3 clinical trial to evaluate the use of RG1068, synthetic human secretin, in pancreatic imaging, as well as increased spending of $202,000 related to our continuing efforts to find a clinical candidate to treat Friedreich’s Ataxia. Significant fluctuations in research and development expenses may occur from period to period depending on the nature, timing, and extent of development activities over any given period of time.

Selling, general and administrative expenses were approximately $1,447,000 and $2,142,000 for the three-month periods ended June 30, 2008 and June 30, 2007, respectively, a decrease of $696,000 or 32%. This decrease is largely attributable to a $770,000 decrease in litigation expenses related to our patent infringement settlement with Bristol, partially offset by increased headcount and recruiting costs as we expand our business development and other functions to support the business.

Interest income

Interest income was approximately $532,000 and $257,000 for the three-month periods ended June 30, 2008 and June 30, 2007, respectively. The increase is primarily due to a significantly higher investment balance for the three months ended June 30, 2008 as a result of the funds received from the Settlement Agreement with ImClone Systems, Incorporated (“ImClone”).

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Income Tax Provision

The Company had income before taxes of approximately $8,489,000 and $240,000 in the three-month periods ended June 30, 2008 and June 30, 2007, respectively. The Company provided approximately $210,000 and $0 for income taxes in the three-month periods ended June 30, 2008 and June 30, 2007, respectively. Prior to the $40.2 million litigation gain from the ImClone Settlement in the second quarter of fiscal 2008, the company had net operating losses and other research credits that reduced our effective tax rate to zero. For fiscal year 2009, we anticipate an effective tax rate of approximately 2.5%. The effective tax rate differs from the statutory tax rate due to the continued utilization of prior year net operating losses and credits, offset by the effects of the alternative minimum tax (“AMT”) on income derived during the fiscal year.

The Company has net operating loss carryforwards of approximately $63,517,000, business tax credits carryforwards of approximately $2,205,000, and other tax credits of approximately $733,000 available to reduce future federal income taxes, if any. Additionally, the Company also has business tax credits carryforwards of approximately $2,665,000 available to reduce future state income taxes, if any. The Company has utilized all available state net operating loss carryforwards. The net operating loss and business tax credits carryforwards will continue to expire at various dates through March 2026. 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.

As of June 30, 2008, a full valuation allowance has been provided against the net operating losses, business tax credits and other deferred tax assets, as it is uncertain if the Company will realize the benefits of such deferred tax assets.

Liquidity and capital resources

We have financed our operations primarily through sales of equity securities, revenues derived from product sales and grant and research agreements and more recently from consideration received as a result of the successful settlement of litigation. Our revenue for the foreseeable future will be primarily limited to our product revenue related to Protein A, royalties from Bristol for their United States net sales of Orencia^®, research grants and other revenue. Revenues derived from the sales of SecreFlo^® vials are expected only through the second quarter of fiscal year 2009. 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. Total cash, cash equivalents and marketable securities at June 30, 2008 totaled approximately $66,126,000, an increase of $5,537,000 from $60,589,000 at March 31, 2008.

Operating activities

Our operating activities provided cash of approximately $5,637,000 for the three-month period ended June 30, 2008. Cash provided by operations is primarily due to net income of $8,279,000, plus certain non-cash expenses such as $241,000 for depreciation and $160,000 in stock-based compensation expense, offset by a $1,273,000 increase in accounts receivable and a $1,788,000 decrease in accounts payable. Accounts receivable increased as a result of the $1,566,000 royalty revenue from Bristol for Orencia^® sales through June 30, 2008 which was recognized when earned but is not due until after quarter end, offset by improved collections in our trade receivables. The decrease in accounts payable and accrued expenses from year end was largely the result of the payment of outstanding legal invoices associated with the Bristol litigation that was completed in April 2008.

Investing activities

Our investing activities consumed approximately $4,974,000 for the three-month period ended June 30, 2008 as we made $4,641,000 net purchases of marketable securities, investing the funds provided by our operating activities above. In addition, the Company invested approximately $333,000 in equipment purchases and improvements to the Company’s facility.

Financing activities

Stock option exercises provided cash proceeds of approximately $234,000 for the three months ended June 30, 2008.

We do not currently use derivative financial instruments. We generally place our marketable security investments in high quality credit instruments as specified in our investment policy guidelines.

Working capital increased to approximately $51,476,000 at June 30, 2008 from $49,831,000 at March 31, 2008 due to the increases in cash and receivables as well as the decrease in accounts payable noted above.

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

• the success of our clinical studies;

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

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• our ability to acquire additional product candidates;

• the success of any proposed financing efforts; and

• the ability to sustain sales and profits of our commercial products.

Absent acquisitions of additional products, product candidates or intellectual property, we believe our current cash and investment balances are adequate to meet our needs. Our future capital requirements include, but are not limited to, continued investment in our research and development programs, capital expenditures primarily associated with purchases of equipment and facilities and continued investment in our intellectual property portfolio.

We plan to continue to invest in key research and development activities. We actively evaluate various strategic transactions on an ongoing basis, including 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 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.

Off-Balance Sheet Arrangements

As of June 30, 2008, we did not have any off-balance sheet arrangements.

Commitments

As of June 30, 2008, 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	$	2,136	$	660	$	1,201	$	275	$	—
Capital lease obligations (1)		84		43		41		—		—
Purchase obligations (2)		1,498		1,498		—		—		—
Contractual obligations (3)		431		118		207		86		20
Total	$	4,149	$	2,319	$	1,449	$	361	$	20

(1) Represents principal payments only; principal and interest are payable through a fixed annual payments of approximately $48,000.

(2) Represents purchase orders for the procurement of raw material for manufacturing as well as clinical materials to support our upcoming trials.

(3) Includes payments for license, supply and consulting agreements.

Cautionary Statement Regarding Forward-Looking Statements

Statements in this Quarterly Report on Form 10-Q, as well as oral statements that may be made by Repligen or by officers, directors or employees of Repligen acting on its behalf, that are not historical facts constitute “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 forward-looking statements in this Quarterly Report on Form 10-Q do not constitute guarantees of future performance. Investors are cautioned that statements in this Quarterly Report on Form 10-Q which are not strictly historical statements, including, without limitation, statements regarding current or future financial performance, management’s strategy, litigation strategy, costs of legal proceedings, disputes with suppliers, plans and objectives for future operations, clinical trials and results, marketing plans, revenue potential of therapeutic product candidates, product research, intellectual property and development, manufacturing plans and performance, delays in manufacturing by us or our partners, timing of customer orders, the anticipated growth in our target markets, including, without limitation, the market for neuropsychiatric disorders treatment, the market for pancreatic disease treatment, the monoclonal antibody market and the process chromatography industry and projected growth in product sales, costs of operations, sufficiency of funds to meet management objectives and availability of financing and effects of accounting pronouncements constitute forward-looking statements. Such forward-looking statements involve known and unknown risks, uncertainties and other factors that could cause our actual results to be materially different from the historical

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results or from any results expressed or implied by such forward-looking statements, including, without limitation, risks associated with: the success of current and future collaborative relationships, the success of our clinical trials and our ability to develop and commercialize products, our ability to obtain required regulatory approvals, our compliance with all Food and Drug Administration regulations, our ability to obtain, maintain and protect intellectual property rights for our products, the risk of litigation regarding our patent and other intellectual property rights, the risk of litigation with collaborative partners, our limited sales and marketing experience and capabilities, our limited manufacturing capabilities and our dependence on third-party manufacturers and value-added resellers, our ability to hire and retain skilled personnel, the market acceptance of our products, our ability to compete with larger, better financed pharmaceutical and biotechnology companies that may develop new approaches to the treatment of our targeted diseases, our history of losses and expectation of incurring continued losses, our ability to generate future revenues, our ability to raise additional capital to continue our drug development programs, our volatile stock price, and the effects of our anti-takeover provisions. Further information on potential risk factors that could affect our financial results are included in the filings made by us from time to time with the Securities and Exchange Commission including under the section entitled “Risk Factors” in our Annual Report on Form 10-K for the year ended March 31, 2008.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURE ABOUT MARKET RISK

Interest Rate Risk

We have investments in commercial paper, U.S. Government and agency securities, 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 increase in interest rates would result in an approximate $253,000 decrease in the fair value of our investments as of June 30, 2008. 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. We intend to hold the majority of our investments to maturity, in accordance with our business plans.

ITEM 4. CONTROLS AND PROCEDURES

The Company’s management, with the participation of the chief executive officer and the 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 Securities Exchange Act of 1934, as amended (the “Exchange Act”)) as of the end of the period covered by this report. Based on such evaluation, the chief 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 in ensuring that information required to be disclosed by the Company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, on a timely basis, and is accumulated and communicated to the Company’s management, including the Company’s chief executive officer and the Company’s principal financial officer, as appropriate to allow timely decisions regarding required disclosure.

There was no change in the Company’s internal control over financial reporting that occurred during the period covered by this Quarterly Report on Form 10-Q that has materially affected, or is reasonably likely to materially affect, the Company’s internal control over financial reporting.

PART II. OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

In January 2006, Repligen and the University of Michigan jointly filed a complaint against Bristol in the United States District Court for the Eastern District of Texas for infringement of the ‘941 patent for the commercial sale of Orencia^®. The ‘941 patent, entitled “Methods of Treating Autoimmune Disease via CTLA4-Ig,” covers methods of using CTLA4-Ig to treat rheumatoid arthritis, as well as other therapeutic methods. Repligen has exclusive rights to this patent from its owners, the University of Michigan and the U.S. Navy. In February 2006, Bristol answered the complaint and counterclaimed seeking a declaratory judgment that the ‘941 patent is invalid and unenforceable and that Bristol does not infringe the patent.

On April 7, 2008, Repligen and the University of Michigan entered into a settlement agreement (the “Bristol Settlement”) with Bristol. Pursuant to the Bristol Settlement, Bristol made an initial payment of $5 million to Repligen. The Bristol Settlement further provides for Bristol to pay 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% of annual sales in excess of $1 billion for each year until December 31, 2013. The Bristol Settlement served as the basis for Repligen and the University of Michigan to dismiss the lawsuit against Bristol and for Repligen and the University of Michigan to grant to Bristol an exclusive worldwide license to the ‘941 patent and certain other intellectual property.

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Other

From time to time, we may be subject to other 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 1A. RISK FACTORS

None.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

In June 2008, the Board of Directors authorized a program to repurchase up to 1.25 million 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 publicly announced the stock repurchase program on June 18, 2008. The Company did not repurchase any securities under this program as of June 30, 2008.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

None.

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

None.

ITEM 5. OTHER INFORMATION

None.

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ITEM 6. EXHIBITS

(a) Exhibits

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). (File No. 000-14656)
3.2	Certificate of Designation of Series A Junior Participating Preferred Stock dated March 4, 2003 (filed as Exhibit A of Exhibit 1 to Repligen Corporation’s Registration Statement on Form 8-A filed March 4, 2003 and incorporated herein by reference). (File No. 000-14656)
3.3	Amended and Restated By-laws (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). (File No. 000-14656)
10.1+	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.
31.1+	Rule 13a-14(a)/15d-14(a) Certification of Principal Executive Officer.
31.2+	Rule 13a-14(a)/15d-14(a) Certification of Principal Financial and Accounting Officer.
32.1+	Certification of Principal Executive Officer and Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

+ Filed herewith.

20

SIGNATURE

Pursuant to the requirements 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: August 8, 2008	By:	/s/ Walter C. Herlihy
		Walter C. Herlihy
		Chief Executive Officer and President
		(Principal Executive Officer)
		Repligen Corporation
Date: August 8, 2008	By:	/s/ William J. Kelly
		William J. Kelly
		Vice President Finance and Administration
		(Principal Financial and Accounting Officer)
		Repligen Corporation

21

EXHIBIT INDEX

EXHIBIT	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). (File No. 000-14656)
3.2	Certificate of Designation of Series A Junior Participating Preferred Stock dated March 4, 2003 (filed as Exhibit A of Exhibit 1 to Repligen Corporation’s Registration Statement on Form 8-A filed March 4, 2003 and incorporated herein by reference). (File No. 000-14656)
3.3	Amended and Restated By-laws (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). (File No. 000-14656)
10.1+	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.
31.1+	Rule 13a-14(a)/15d-14(a) Certification of Principal Executive Officer.
31.2+	Rule 13a-14(a)/15d-14(a) Certification of Principal Financial and Accounting Officer.
32.1+	Certification of Principal Executive Officer and Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

+ Filed herewith.

22

EX-10.1

Exhibit 10.1

EXECUTION COPY

SETTLEMENT AND RELEASE AGREEMENT

THIS SETTLEMENT AND RELEASE AGREEMENT (the “Agreement”) is made and entered into as of April 7, 2008 (the “Effective Date”) by and between Repligen Corporation, a Delaware corporation having offices at 41 Seyon Street, Building #1, Suite 100, Waltham, MA 02453, The Regents of the University of Michigan having offices at 1214 S. University Ave., 2^nd Floor, Ann Arbor, MI 48104 and Bristol-Myers Squibb Company, a Delaware corporation having offices at Route 206 & Province Line Road, Princeton, NJ 08543.

RECITALS

WHEREAS, BMS has commercialized the drug product ORENCIA^® (Abatacept) that contains a fusion protein that consists of the extracellular domain of human CTLA4 linked to the modified Fc portion of human immunoglobulin G1, for therapeutic use in humans;

WHEREAS, UM and Repligen own and/or control certain patent rights relating to CTLA4 and its therapeutic use;

WHEREAS, in connection with the settlement of the Pending Action, BMS wishes to obtain license rights under certain patent rights owned and/or controlled by Licensors for certain products, including but not limited to Abatacept and products containing Abatacept;

WHEREAS, UM and Repligen are willing to grant and consent to (to the extent the consent of either is required) the license rights to BMS on the terms and conditions set forth below;

WHEREAS, Repligen and UM filed the Pending Action against BMS in the United States District Court for the Eastern District of Texas, Case No. 2:06-cv-4-TJW, alleging claims relating to infringement of U.S. Patent No. 6,685,941;

WHEREAS, BMS denied infringing U.S. Patent No. 6,685,941 due to invalidity, unenforceability, and/or contractual rights; and

WHEREAS, Repligen, UM and BMS desire to enter an agreement to settle the Pending Action and resolve any and all patent infringement disputes related to the Pending Action in order to avoid further litigation risks and expenses and to seek an amicable and final business resolution and settlement of the Pending Action.

NOW, THEREFORE, in consideration of the above premises which are an integral part of this Agreement and incorporated fully herein, and the promises and the mutual covenants recited herein, the Parties agree as follows.

ARTICLE 1

DEFINITIONS

The terms in this Agreement with initial letters capitalized, whether used in the singular or the plural, shall have the meaning set forth below or, if not listed below, the meaning designated in places throughout this Agreement.

1.1 “Affiliate” means any Person that (directly or indirectly) through one or more intermediaries, controls, is controlled by, or is under common control with the Party specified. For the purposes of this definition, “control” shall mean the possession, direct or indirect, of the power to cause the direction of the management and policies of a Person, whether through ownership of fifty percent (50%) or more of the voting securities of such Person, by contract or otherwise.

1.2 “Belatacept” means the fusion protein known as Belatacept (also known as LEA29Y), and any pharmaceutical product containing such protein.

1.3 “BMS” means Bristol-Myers Squibb Company.

1.4 “BMS Released Parties” and “BMS Releasor” means BMS’s agents, servants, attorneys, employees, officers, directors, Affiliates, predecessors, successors, assigns, licensors, transferees (including but not limited to Sublicensees), representatives and all persons and entities acting by, through, under, or in concert with them or any of them (but excluding Licensor or any Licensor Releasor to the extent that such Licensor or Licensor Releasor would otherwise become a BMS Released Party or BMS Releasor by virtue of a right or license granted in or pursuant to this Agreement).

1.5 “Business Day” or “business day” means a day other than Saturday, Sunday or any day on which commercial banks located in New York, New York are authorized or obligated by applicable laws to close.

1.6 “Calendar Quarter” means each three month period commencing January 1, April 1, July 1 and October 1 of each year during the term of this Agreement.

1.7 “Calendar Year” means each successive period of 12 months commencing on January 1 and ending on December 31.

1.8 “Combination Product” means a Product that includes at least one additional active ingredient (whether coformulated or copackaged) (which is not a protein as defined in Section 1.28 below) in addition to the protein as defined in Section 1.28. Drug delivery vehicles, adjuvants, and excipients shall not be deemed to be “active ingredients”, except in the case where such delivery vehicle, adjuvant, or excipient is recognized by the FDA as an active ingredient in accordance with 21 CFR 210.3(b)(7).

1.9 “Controlled” or “Controls” means, with respect to any Patent, possession by a Licensor of the right, whether directly or indirectly, and whether by ownership, license or otherwise, to grant a license or sublicense or covenant not to sue under such Patent to BMS as provided for herein without violating the terms of any agreement in effect as of the Effective Date with any Third Party.

1.10 “CTLA4” means cytotoxic T lymphocyte-associated antigen 4.

1.11 “Dollar” or “$” means the lawful currency of the United States.

1.12 “Effective Date” shall have the meaning set forth in the preamble of this Agreement.

1.13 “Field” means the diagnosis, treatment, control or prevention of any human disease, disorder or condition.

1.14 “GAAP” means U.S. Generally Accepted Accounting Principles.

1.15 “HHMI” means the Howard Hughes Medical Institute.

1.16 “Licensed CTLA4 Product” means (i) any protein (including a fusion protein) that contains all or a portion of the extracellular domain of CTLA4, (ii) any other soluble CTLA4 molecule and (iii) CTLA4 antibodies; and any pharmaceutical product containing any of the foregoing. For clarity, “Licensed CTLA4 Product” includes without limitation Belatacept and Product.

1.17 “Licensed Patents” means the Thompson Patent Rights and the Other Patents.

1.18 “Licensor” means each of Repligen and UM individually. “Licensors” means Repligen and UM collectively.

1.19 “Licensor Releasor” and “Licensor Released Parties” means for each Licensor, their respective agents, servants, attorneys, employees, officers, directors, Affiliates, predecessors, successors, assigns, licensors, transferees, representatives and all persons and entities acting by, through, under, or in concert with them or any of them (but excluding BMS or any BMS Releasor to the extent that BMS or such BMS Releasor would otherwise become a Licensor Released Party or Licensor Releasor by virtue of a right or license granted in or pursuant to this Agreement).

1.20 “Navy” means individually and collectively the United State Department of the Navy, the Naval Medical Research Center and/or The United States of America as represented by the Secretary of the Navy.

1.21 “Navy License Agreement” means the Exclusive License Agreement between Repligen and the United States Department of the Navy at the Naval Medical Research Center (signed by Repligen on December 19, 2003) relating to U.S. Patent Application 08/385,194 and any amendments thereto.

1.22 “Net Sales” means, as to each Calendar Quarter, the gross invoiced sales prices charged for all Product sold in the U.S. during such Calendar Quarter, by or for BMS, its Affiliates and Sublicensees to Third Parties, after deduction (if not already deducted in the amount invoiced and only to the extent that such sums are otherwise included in the gross invoiced sales price) of the following items actually incurred by BMS, its Affiliates or Sublicensees during such Calendar Quarter with respect to such sales of Product in that Calendar Quarter:

(a) trade, cash, and/or quantity discounts, retroactive price reductions, charge-back payments and rebates actually taken and allowed, including discounts or rebates to governmental or managed care organizations;

(b) credits or allowances given or recorded for rejection or return of previously sold Product (including, without limitation, returns of Product in connection with recalls or withdrawals);

(c) any tax, tariff, duty or government charge (including any tax such as a value added or similar tax or government charge other than an income tax) levied on the sale, transportation or delivery of a Product and borne by the seller thereof without reimbursement from any third party;

(d) freight out, postage, shipping and insurance charges for delivery of such Product if separately set out on the invoice; and

(e) amounts written off by reason of uncollectible debt.

Net Sales and all of the foregoing deductions from the gross invoiced sales prices of Product shall be determined in accordance with BMS’s standard accounting procedures and in accordance with GAAP. In the event that BMS, its Affiliates or Sublicensees make any adjustments to such deductions after the associated Net Sales have been reported pursuant to this Agreement, the adjustments shall be reported and reconciled with the next report and payment of any royalties due under Article 4. A Product shall be considered “sold” when it is invoiced, shipped or paid for, whichever shall occur first.

In the case of any Combination Product sold in the U.S., Net Sales for such Combination Product shall be calculated by multiplying actual Net Sales of such Combination Product by the fraction A/(A+B) where A is the invoice price of the Product if sold separately without the other active ingredient(s), and B is the total invoice price of the other active ingredient(s) in the Combination Product, if sold separately. If such other active ingredient(s) in the Combination Product are not sold separately, Net Sales for the purpose of determining royalties of the Combination Product shall be calculated by multiplying actual Net Sales of such Combination Product by the fraction A/D, where A is the invoice price of the Product if sold separately, and D is the invoice price of the Combination Product. If neither the Product nor such other active ingredient(s) is sold separately, the Parties shall in good faith, determine Net Sales for such Combination Product by mutual agreement.

For avoidance of doubt, Net Sales shall be determined as set forth above based on sales of the Product in the U.S. only. Sales of Product outside of the U.S. shall not be included in the determination of Net Sales.

1.23 “Other Patents” means, with respect to each Licensor, all Patents Controlled by such Licensor as of the Effective Date, other than the Thompson Patent Rights, upon which such Licensor (or any Third Party obtaining rights to such Patents) could assert, now or in the future, a claim of infringement based on the manufacture, use, sale, offer for sale, exportation and/or importation of any Licensed CTLA4 Product. For clarity, Other Patents shall include: (i) all Patents filed after the Effective Date which claim priority to any of the foregoing Patents, to the extent they cover subject matter disclosed and/or claimed in the foregoing Patents; and (ii) any patent(s), other than the Thompson Patent Rights, issuing anywhere in the world from any application (including, but not limited to, divisionals, continuations, continuations-in-part and renewals) that (1) is pending on or after the Effective Date and (2) claims priority (directly or indirectly) to the application from which U.S. Patent No. 6,685,941 issued or any application to which U.S. Patent No. 6,685,941 claims priority, wherein the manufacture, use, sale, offer for sale, exportation and/or importation of any Licensed CTLA4 Product would infringe an issued claim or claims thereof.

1.24 “Party” means either Repligen, UM or BMS. “Parties” means collectively Repligen, UM and BMS.

1.25 “Patents” means (a) patents and patent applications in any country or jurisdiction, (b) all direct and indirect priority applications, divisionals, continuations, and continuations-in-part of any of the foregoing, and (c) all patents issuing on any of the foregoing patent applications; together with all registrations, reissues, renewals, re-examinations, confirmations, supplementary protection certificates and extensions, and applications therefor, of any of (a), (b) or (c).

1.26 “Pending Action” means the action pending as of the Effective Date between the Parties in the United States District Court for the Eastern District of Texas, Case No. 2:06-cv-4-TJW, relating to U.S. Patent No. 6,685,941.

1.27 “Person” means any individual, firm, corporation, partnership, limited liability company, trust, business trust, joint venture company, governmental authority, association or other entity.

1.28 “Product” means a fusion protein that contains the extracellular domain of the human CTLA4, where such protein binds to CD80 (B7-1) and/or CD86 (B7-2), and any pharmaceutical product that contains such a protein in any form, formulation, dosage or presentation. Pharmaceuticals that contain the same active ingredient shall be considered the same “Product” as one another even if marketed for different indications. Product shall exclude Belatacept and pharmaceutical products containing Belatacept. Product shall include Abatacept and the pharmaceutical product containing Abatacept being sold by BMS under the trademark ORENCIA^®.

1.29 “Prosecution and Maintenance” means (a) preparing, filing and prosecuting patent applications (including, but not limited to, reissue, reexamination, continuation, continuation-in-part, divisional, and substitute applications and any foreign counterparts thereof, and extensions of the foregoing); (b) maintaining patent applications and patents; and (c) managing interferences, oppositions or similar administrative proceedings relating to any of the foregoing, and any civil action relating to the inventorship, validity or patentability of a patent or patent application that does not include a claim of patent infringement (including, but not limited to, the preparation and filing of all documents and participation in all oral hearings in connection with all the foregoing).

1.30 “Repligen” means Repligen Corporation and its Affiliates.

1.31 “Royalty Term” means the period beginning on January 1, 2008 and ending on the earlier of (i) December 31, 2013 or (ii) at such time that all claims of U.S. Patent No. 6,685,941 have been disclaimed, abandoned, lapsed or dedicated to the public or held revoked, unenforceable, unpatentable or invalid (whether through reexamination, reissue, opposition or otherwise) by a decision of a court or governmental agency of competent jurisdiction, which decision is unappealable or unappealed within the time allowed for appeal, provided that such decision does not result from any action taken by BMS or any Person acting on the behalf of, with the assistance of, or in concert with BMS.

1.32 “Sublicensee” means any Third Party which is sublicensed by BMS or any of its Affiliates to market and sell Product, but shall not include any wholesaler or distributor.

1.33 “Territory” means the entire world.

1.34 “Third Party” means any Person other than Repligen and its Affiliates, UM and BMS and BMS’s Affiliates.

1.35 “Thompson Patent Rights” means (i) U.S. Patent No. 6,685,941 issued February 3, 2004; (ii) any foreign counterpart of U.S. Patent No. 6,685,941, (iii) any patent(s) issuing anywhere in the world from any application (including, but not limited to, divisionals, continuations, continuations-in-part and renewals) claiming priority (directly or indirectly) to U.S. Patent No. 6,685,941, PCT/US93/03155, PCT/US94/06701, U.S. Ser. No. 08/385,194, U.S. Ser. No. 08/076,071, U.S. Ser. No. 12/044,679 and/or U.S. Ser. No. 10/714,055; (iv) any patents that are reissues, reexaminations, extensions, or foreign counterparts of any of the foregoing; and (v) any application from which any of the foregoing patents issue; in each case for clauses (ii) through (v), to the extent that such application or patent covers the manufacture, use, sale, offer for sale, exportation and/or importation of any Licensed CTLA4 Product.

1.36 “UM” means The Regents of the University of Michigan.

1.37 “U.S.” and “United States” means the United States of America, including its territories and possessions.

1.38 “Written Approval Letter” means the written letter agreement between Repligen and the Navy dated April 7, 2008.

ARTICLE 2

LICENSE GRANT, SETTLEMENT AND RELEASE

2.1 License. Subject to the terms and conditions of this Agreement, Repligen hereby grants to BMS an exclusive, worldwide license, with the right to grant sublicenses (in accordance with Section 2.2), under the Thompson Patent Rights and the Other Patents to make, have made, use, sell, have sold, offer for sale, import and/or export Licensed CTLA4 Product (including but not limited to Product and Belatacept) in the Territory in the Field. Subject to the terms and conditions of this Agreement, UM hereby grants, except to the extent that it has already granted such rights to Repligen (in which case UM hereby consents to the foregoing grant of rights by Repligen to BMS), to BMS an exclusive, worldwide license, with the right to grant sublicenses (in accordance with Section 2.2), under the Thompson Patent Rights and the Other Patents to make, have made, use, sell, have sold, offer for sale, import and/or export Licensed CTLA4 Product (including but not limited to Product and Belatacept) in the Territory in the Field, provided that such license granted by UM under the Other Patents shall be limited to such rights as UM Controls as of the Effective Date.

2.2 Right to Grant Sublicenses. BMS shall have the right to grant, to BMS’s Affiliates and to Third Parties (including but not limited to Sublicensees), sublicenses of the rights granted under Section 2.1 in all or part of the Territory (including on a country-by-country basis); provided that in the case of sublicenses with respect to Product: (a) BMS shall be responsible for the payment of all royalties payable based on the Net Sales of each Product sold by a Sublicensee in accordance with Article 3, (b) any such sublicense shall include (i) a provision granting to BMS audit rights similar to Licensor’s audit rights under Section 4.4 of this Agreement, which rights BMS agrees to exercise for Licensor at Licensor’s request, direction, and expense and (ii) provisions commensurate in scope with Sections 2.4(b), 5.3 and 5.4 of this Agreement, and (c) any such sublicense shall be subject to the reservations in Section 2.6 and 2.7.

2.3 Release and Non-Assertion by Licensors.

(a) In consideration of and subject to the terms and conditions of this Agreement and effective immediately after receipt into Repligen’s account of the funds subject to the wire payment referred to in Section 3.1 below, each Licensor, on behalf of itself and its Licensor Releasors, hereby releases BMS and the BMS Released Parties from any and all claims, demands and rights of action that such Licensor and its Licensor Releasors may have on account of any infringement of any Licensed Patent Controlled by such Licensor (including but not limited to the Thompson Patent Rights) that occurred prior to the Effective Date as a result of the manufacture, use, offer for sale, sale, exportation and/or importation of Licensed CTLA4 Product.

(b) In consideration of and subject to the terms and conditions of this Agreement and effective immediately after receipt into Repligen’s account of the funds subject to the wire payment referred to in Section 3.1 below, each Licensor, on behalf of itself and its Licensor Releasors, covenants not to either directly or indirectly make, file or maintain any claim, demand, lawsuit, action or cause of action, of whatever kind or character, in law or in equity (collectively, a “Claim”) against BMS or any BMS Released Parties, jointly or severally, which Claim asserts that the manufacture, use, sale, offer for sale, import and/or export of Licensed CTLA4 Product infringes any claim of a Licensed Patent Controlled by such Licensor (including but not limited to the Thompson Patent Rights).

(c) In consideration of and subject to the terms and conditions of this Agreement and effective immediately after receipt into Repligen’s account of the funds subject to the wire payment referred to in Section 3.1 below, each Licensor, on behalf of itself and its Licensor Releasors, hereby forever releases BMS and the BMS Released Parties from any and all claims asserted, or that could have been asserted, in the Pending Action.

2.4 Release and Non-Assertion by BMS.

(a) In consideration of and subject to the terms and conditions of this Agreement and effective immediately after receipt into Repligen’s account of the funds subject to the wire payment referred to in Section 3.1 below, BMS, on behalf of itself and its BMS Releasors, hereby releases Licensors and the Licensor Released Parties from any and all claims, demands and rights of action that BMS and its BMS Releasors may have related to the Thompson Patent Rights that arose prior to the Effective Date.

(b) In consideration of and subject to the terms and conditions of this Agreement and effective immediately after receipt into Repligen’s account of the funds subject to the wire payment referred to in Section 3.1 below, BMS, on behalf of itself and its BMS Releasors, covenants not to either directly or indirectly make, file or maintain any claim, demand, lawsuit, action or cause of action, of whatever kind or character, in law or in equity, (including by way of example litigation or administrative proceedings such as reexamination or opposition), challenging the validity or patentability of U.S. Patent 6,685,941 (collectively, a “Patent Challenge”), or assist or act in concert with any Third Party making any such Patent Challenge.

(c) In consideration of and subject to the terms and conditions of this Agreement and effective immediately after receipt into Repligen’s account of the funds subject to the wire payment referred to in Section 3.1 below, BMS, on behalf of itself and the BMS Releasors, hereby forever releases Licensors and the Licensor Released Parties from any and all claims asserted, or that could have been asserted, in the Pending Action.

2.5 Stipulation Of Dismissal. Repligen, UM and BMS shall, within three (3) business days after payment is made pursuant to Section 3.1 below, cause their respective counsel to execute and file in the Pending Action a stipulation of dismissal of all claims and counterclaims with prejudice, pursuant to Rule 41(a), Fed. R. Civ. P., in the form attached hereto as Exhibit A. Each Party shall bear its own costs and fees associated with the Pending Action and no request, motion, petition or otherwise for such fees and/or costs shall be made to the court with respect to the Pending Action.

2.6 Reservation of Rights for the Navy. Licensors reserve for the Navy the rights retained by the Navy in accordance with the terms with the Navy License Agreement as modified by the Written Approval Letter. For clarification, such rights reserved by the Navy are solely with respect to and solely to the extent of the Navy’s ownership interest in the “Licensed Patent”, as such term is defined in the Navy License Agreement, and in no way do any reserved or other rights of the Navy extend to rights in connection with patents or patent applications owned or controlled by BMS outside this Agreement.

2.7 Reservation of Rights for HHMI. Licensors reserve the right for HHMI, solely to the extent that UM has an obligation to reserve such rights for HHMI with respect to such patent rights, to use the Thompson Patent Rights and Other Patents for research and other non-commercial purposes only, without the right to assign or sublicense such right. For avoidance of doubt, no rights are granted expressly or by implication under this Section 2.7 by BMS under any patent rights owned or controlled by BMS (other than such reserved rights under the Thompson Patent Rights and Other Patents).

2.8 No Grant of Rights by BMS. It is expressly understood and agreed that nothing in this Agreement shall be construed as a grant to anyone of any rights under any patents owned or controlled by BMS or to require BMS to grant any such rights in the future.

ARTICLE 3

PAYMENTS AND ROYALTIES

3.1 Payments. Within five (5) business days after the Effective Date, BMS shall pay to Repligen a payment in the amount of five million dollars ($5,000,000).

3.2 Royalty Payments. In consideration of the licenses granted herein, and subject to the other provisions of this Agreement, BMS shall pay to Repligen royalties based on the Net Sales of each Product sold during the Royalty Term. The royalty payable with respect to each particular Product shall be based on the level of aggregate annual Net Sales of such Product in a given Calendar Year period by BMS, its Affiliates and Sublicensees, with the royalty rate tiered based upon the level of such aggregate Net Sales in such Calendar Year period as follows:

1.8% of annual Net Sales less than or equal to $500 million;

2% of annual Net Sales greater than $500 million and less than or equal to $1 billion;

4% of annual Net Sales greater than $1 billion.

Royalties shall be calculated using the applicable royalty rate or rates set out above and shall be determined based on the annual Net Sales of the Product for the Calendar Year in question, and shall be paid at the rate applicable to the portion of Net Sales within each of the above Net Sales tiers during such Calendar Year. By way of example, for a Product in a given Calendar Year period, if the total Net Sales of such Product in such Calendar Year period is $1.2 billion, the royalty payable by BMS to Repligen will be (1.8% x $500 million) + (2% x $500 million) + (4% x $200 million) = $27 million.

3.3 Sales To or Between BMS, its Affiliates and Sublicensees. No royalties shall be paid upon sales or transfer of Product to or between any of BMS, its Affiliates, and Sublicensees for further sale, provided that in such case royalties shall be owed upon such further sale of Product in the U.S. by BMS, its Affiliates or Sublicensees to the first independent Third Party.

3.4 No Credit Against Royalties. BMS shall not be entitled to deduct any portion of royalties paid to any third party from the royalties due to Repligen pursuant to this Agreement for any reason.

3.5 One Royalty. Only one royalty shall be payable under this Agreement with respect to the same unit of Product.

3.6 Expanded Access and Donations. No royalties shall accrue on the disposition of Product in reasonable quantities by BMS, its Affiliates or Sublicensees for promotional purposes, as part of an expanded access program or as part of Phase 4 clinical trials or as donations to non-profit institutions or government agencies, except, in each case, to the extent that BMS, its Affiliate or Sublicensees receives payment for such Product.

3.7 Royalty Term. BMS shall have no obligation to make any royalty payments or other payments to Repligen with respect to Net Sales prior to the start of the Royalty Term. For Net Sales after

the end of the Royalty Term, BMS will have no further obligation to make any royalty payments to Repligen under this Agreement and the royalty-bearing licenses and rights granted to BMS by Licensors under this Agreement shall then become fully paid-up and irrevocable, provided that all royalty payments due during the Royalty Term have been paid and the Agreement has not been terminated by any Party prior to the end of the Royalty Term, subject to Article 7.

ARTICLE 4

RECORDS, REPORTS AND PAYMENTS

4.1 Reports. Within forty-five (45) days after the end of each Calendar Quarter, BMS shall furnish to Repligen a written report with respect to the sales of all Product in the U.S. during such Calendar Quarter by BMS, its Affiliates and Sublicensees. Such report shall include (i) the Net Sales and the amount of gross receipts of Product broken down by Product and seller (i.e., BMS, each Affiliate and each Sublicensee) and (ii) the determination of royalty owed (as specified in Article 3) on Net Sales of Product; provided that, in the case where the Effective Date is after March 31, 2008, for Net Sales of Product that occurred during the period of January 1, 2008 through March 31, 2008 (the “First Quarter”), such report for such Net Sales shall be furnished to Repligen within the later of (x) forty-five (45) days after the end of such First Quarter or (y) twenty (20) Business Days after the Effective Date.

4.2 Manner of Payment. Concurrently with each report pursuant to Section 4.1, BMS shall make the royalty payment then due to Repligen. All payments under this Agreement shall be in Dollars and, unless otherwise agreed in writing, shall be made by wire transfer of immediately available funds to:

Citibank, 111 Wall Street, New York, NY

ABA # 021000089

A/C Bear Stearns

A/C # 09253186

Sub A/C : Repligen Corporation

Sub A/C # 220-12132

or such account of Repligen in such bank as Repligen may from time to time designate in writing. All royalty payments shall be free and clear of any taxes, duties, levies, fees or charges.

4.3 Interest. All royalty payments not made when due shall bear interest, calculated from the date such payment was due, at the annual rate of the Bank Prime Loan rate in effect on the date such payment was due plus two percent (2%), as quoted in Federal Reserve Bulletin H.15 or a successor bulletin thereto, from time to time.

4.4 Records. BMS shall keep and shall cause its Affiliates and Sublicensees to keep true, complete and accurate records of all sales of all Product in accordance with GAAP and in sufficient detail to permit Repligen to confirm the accuracy and completeness of BMS’s royalty payments. At Repligen’s request and expense, BMS shall permit, not more than once in a twelve (12) month period, an independent certified public accountant, appointed by Repligen and acceptable to BMS, to examine (and copy to the extent reasonably necessary), at BMS’s principal place of business, upon reasonable notice and at reasonable times and upon such accountant executing an appropriate confidentiality agreement with BMS, such records, solely to the extent necessary to verify the accuracy and completeness of BMS’s royalty payments. BMS shall be responsible for providing access to such records that in the ordinary course of business are in the possession or control of its Affiliates and Sublicensees. Such examination shall be limited to a period of time no more than three (3) years immediately preceding the request for examination. The report of any such examination shall be made simultaneously to Repligen and BMS

and shall simply report the amount, if any, by which BMS has overpaid or underpaid its royalty payments and an explanation of how or why the overpayment or underpayment occurred. If such public accountant correctly concludes that BMS’s royalty payments are in error such that royalties to Repligen were underpaid, then BMS shall promptly (in any event within 20 Business Days) pay the deficiency plus interest pursuant to Section 4.3 to Repligen; and if royalties to Repligen were underpaid by more than seven-and-a-half percent (7.5%) of the total royalty obligation, then BMS shall additionally reimburse Repligen for its reasonable costs incurred in examining such records. Any overpayments by BMS in the three (3) year period immediately preceding the request for such examination shall be fully creditable against amounts payable in subsequent payment periods. If no such amounts become payable following the delivery of such report or if such amounts cannot be credited against amounts payable in subsequent payment periods owing to expiration or termination of this Agreement, then no refund shall be due. In no event shall BMS be entitled to any credit for any overpayment of royalties that occurred prior to such three (3) year period.

ARTICLE 5

REPRESENTATIONS, WARRANTIES, AND DISCLAIMERS

5.1 Mutual Representations and Warranties. Each Party represents and warrants to the other Party that: (i) it has all requisite corporate power and authority to enter into this Agreement and to perform its obligations under this Agreement; (ii) execution of this Agreement and the performance by such Party of its obligations hereunder have been duly authorized; (iii) this Agreement is legally binding and enforceable on each Party in accordance with its terms; and (iv) the performance of this Agreement by it does not create a breach or default under or conflict with any other agreement or obligation to which it is a Party, or violate any applicable law, order, rule or regulation.

5.2 Representations and Warranties of Licensor. Each Licensor represents and warrants to BMS that:

(a) it has the full right, power, and corporate authority to enter into this Agreement and to make the covenants and grant the rights and licenses set forth in this Agreement, and that this Agreement is enforceable against it in accordance with its terms;

(b) UM and the Navy are the joint owners of all right, title, and interest in and to U.S. Patent No. 6,685,941;

(c) Repligen is the exclusive licensee with respect to Thompson Patent Rights and Licensors jointly have the full legal right, power and ability to extend the rights and grant the exclusive licenses in, to and for the Thompson Patent Rights to BMS as set forth in this Agreement;

(d) Licensor is not a party to any agreement or other binding commitment or obligation of any kind, the terms of which (i) conflict with the covenants and obligations of Licensor under this Agreement or the rights granted by Licensor to BMS under this Agreement or (ii) derogates from the rights granted by Licensor to BMS in this Agreement or the ability of Licensor to perform its covenants and obligations under this Agreement;

(e) except for the exclusive license granted by UM to Repligen, and the rights of HHMI under Section 2.2 of the License Agreement dated July 24, 2000 between Repligen and UM, as of the Effective Date, no Third Party holds any license and/or any option for a license and/or the grant of a covenant not to sue, from UM with respect to the Thompson Patent Rights;

(f) as of the Effective Date, no Third Party holds any license and/or any option for a license and/or the grant of a covenant not to sue, from Repligen with respect to the Thompson Patent Rights,

(g) it will not after the Effective Date enter into any agreements, contracts or other arrangements, or relinquish any rights, that would be inconsistent with or in conflict with or in derogation of BMS’s rights and licenses under this Agreement or Licensor’s obligations under this Agreement, except as provided in Section 8.1 and without limiting Section 8.2;

(h) Craig B. Thompson (co-inventor of U.S. Patent No. 6,685,941) has assigned all of his rights with respect to the Thompson Patent Rights to UM;

(i) Carl H. June (co-inventor of U.S. Patent No. 6,685,941) has assigned all of his rights with respect to the Thompson Patent Rights to The United States of America as represented by the Secretary of the Navy and/or UM;

(j) Repligen and/or UM has entered into enforceable written agreement(s) with the Navy granting to Repligen exclusive rights with respect to the rights and interest of Carl H. June and the Navy with respect to the Thompson Patent Rights which enables Licensors to grant the exclusive license to BMS under this Agreement, subject only to the rights retained by the Navy in accordance with the terms with the Navy License Agreement as modified by the Written Approval Letter;

(k) no Third Party has any rights to enforce the Thompson Patent Rights;

(l) it has not entered into any agreements, or relinquished any rights, related to the Thompson Patent Rights or Other Patents between March 5, 2008 and the Effective Date of this Agreement, with any Third Party, other than the Navy and except as provided in Section 8.1;

(m) it will maintain, fully perform its obligations and will not relinquish any of its rights under any agreements existing as of the Effective Date granting or transferring any rights to it with respect to the Thompson Patent Rights or Other Patents, except as provided in Section 8.1 and without limiting Section 8.2;

(n) with respect to any and all agreements of Licensor through which Licensor has acquired or holds any rights to the Thompson Patent Rights: the rights under each such agreement are and shall remain in full force and effect; Licensor has not committed any act or failed to do any act that would constitute a breach of the agreement or provide any Person with a right to terminate the agreement; and Licensor will provide BMS with any notice of default or deficiency received from any party to the agreement at least 20 days prior to the expiration of any period allowed to cure the default or deficiency, and thereafter BMS shall have the right (but not the obligation or responsibility) to cure the alleged default or deficiency and to deduct any payment made for that purpose from the next royalty payment(s) due to Repligen under Article 3 but only if such default or deficiency is cured through a monetary payment;

(o) prior to the Effective Date it has obtained any necessary approval from HHMI to enter into and grant the rights and licenses to BMS under this Agreement; and

(p) prior to the Effective Date Repligen has provided BMS with a copy of the Written Approval Letter.

5.3 Disclaimer. Nothing in this Agreement is or shall be construed as:

(a) a warranty or representation by Licensor as to the validity, enforceability, or scope of any claim or patent or patent application within the Licensed Patents in the Territory;

(b) subject to the representations and warranties of Licensor under Section 5.2, a warranty or representation by Licensor that anything made, used, sold, or otherwise disposed of under any

license granted in this Agreement is or will be free from infringement of any patent rights or other intellectual property right of any Third Party;

(c) a grant by Licensor, whether by implication, estoppel, or otherwise, of any licenses or rights, under any patent or patent application, or under any know-how or other right, other than that expressly granted under Article 2;

(d) an obligation by any Party to bring or prosecute actions or suits against any Third Party for infringement of any of the Licensed Patents; or

(e) a representation or acknowledgement by BMS that any claim of any patent or patent application within the Licensed Patents is or has been infringed by any product or activity.

5.4 Further Disclaimer. NO WARRANTY IS GIVEN WITH RESPECT TO THE LICENSED PATENTS, EXPRESS OR IMPLIED, EITHER IN FACT OR BY OPERATION OF LAW, BY STATUTE OR OTHERWISE, AND THE PARTIES SPECIFICALLY DISCLAIM ANY EXPRESS OR IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, VALIDITY OF THE LICENSED PATENTS, OR NON-INFRINGEMENT OF THE PATENT OR OTHER RIGHTS OF ANY THIRD PARTY.

5.5 IN NO EVENT SHALL ANY PARTY, INCLUDING THEIR REGENTS, FELLOWS, OFFICERS, EMPLOYEES AND AGENTS, BE RESPONSIBLE OR LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR PUNITIVE DAMAGES OR LOST PROFITS, LOSS OF OPPORTUNITY, OR OTHER ECONOMIC LOSS OR DAMAGE WITH RESPECT TO ANY CAUSE OF ACTION ARISING OUT OF THIS AGREEMENT, REGARDLESS OF LEGAL OR EQUITABLE THEORY, PROVIDED, HOWEVER, THAT (i) NOTHING IN THIS SECTION 5.5 SHALL IN ANY WAY MODIFY OR OTHERWISE AFFECT BMS’S OBLIGATION TO PAY ROYALTIES IN ACCORDANCE WITH THE PROVISIONS OF THIS AGREEMENT, NOR LIMIT LICENSORS’ RIGHT TO SEEK AND RECOVER FULL DAMAGES FOR ANY UNPAID ROYALTIES FROM BMS, ITS AFFILIATES OR SUBLICENSEES AND (ii) THERE SHALL BE NO LIMITATION ON AVAILABLE REMEDIES AND THIS SECTION 5.5 SHALL NOT APPLY WITH RESPECT TO ANY CAUSE OF ACTION BASED ON THE WILLFUL, INTENTIONAL, RECKLESS AND/OR GROSSLY NEGLIGENT BREACH OF ANY OBLIGATION, REPRESENTATION, WARRANTY AND/OR COVENANT UNDER THIS AGREEMENT BY A PARTY.

ARTICLE 6

INDEMNIFICATION

6.1 BMS Indemnification. Subject to Section 6.2, BMS shall indemnify, defend and hold Repligen, and their respective directors, trustees, officers, employees and agents (collectively, the “Indemnitee”) harmless from and against any and all liabilities, claims, demands, expenses (including, without limitation, attorneys and professional fees and other costs of litigation), losses or causes of action (each, a “Liability”) arising out of or relating in any way to (i) the possession, manufacture, use, sale or other disposition of Product or Licensed CTLA4 Product by BMS, its Affiliates and Sublicensees hereunder, whether based on breach of warranty, negligence, product liability or otherwise, (ii) subject to Section 8.3, the exercise of any right granted to BMS pursuant to this Agreement, or (iii) any breach of this Agreement by BMS, its Affiliates and Sublicensees except to the extent, in each case, that such Liability is caused by (x) the negligence or willful misconduct of a Licensor and/or the Indemnitee (or its directors, officers, employees and agents) seeking protection under this provision or (y) a Licensor’s material breach of this Agreement or any representation or warranty under this Agreement.

6.2 Indemnification Procedure. A claim to which indemnification applies under Section 6.1 or 6.2 shall be referred to herein as an “Indemnification Claim”. If an Indemnitee intends to claim indemnification under this Article 6, the Indemnitee or the appropriate Licensor shall notify BMS in writing promptly upon becoming aware of any claim that may be an Indemnification Claim. BMS shall have the right to assume and control the defense of the Indemnification Claim at its own expense with counsel selected by BMS, provided, however, that an Indemnitee or the appropriate Licensor shall have the right to retain its own counsel, with the fees and expenses to be paid by the Indemnitee, if Indemnitee determines that representation of such Indemnitee by the counsel retained by BMS would be inappropriate due to actual or potential differing interests between such Indemnitee and any party represented by such counsel in such proceedings. BMS shall have the right to settle or compromise any claims for which it is providing indemnification under this Article 6, provided that the consent of the Indemnitee (which shall not be unreasonably withheld, delayed or conditioned) shall be required in the event any such settlement or compromise would adversely affect the interests of the Indemnitee. The indemnification obligations of BMS under this Article 6 shall not apply to amounts paid in settlement of any loss, claim, damage, liability or action if such settlement is effected without the consent of BMS. The failure to deliver notice to BMS within a reasonable time after the commencement of any action subject to this Article 6, if materially prejudicial to BMS’s ability to defend such action, shall relieve BMS of any obligation to the Indemnitee under this Article 6 with respect to Liability relating to or arising from such action. The Indemnitee and its employees and agents, shall reasonably cooperate with BMS and its legal representatives in the investigation of any action, claim or liability covered by this indemnification.

6.3 UM Indemnification. UM shall indemnify, defend and hold BMS and its directors, officers and employees harmless from and against any and all liabilities, claims, demands, expenses (including, without limitation, reasonable attorneys fees and other costs of litigation), losses or causes of action (“UM Liabilities”) arising out of or relating in any way to UM’s entering into this Agreement and the terms hereof, and specifically including without limitation any claim, demand or assertion of rights against BMS or those in privity with it by any party with whom UM has an agreement (including HHMI) relating to any patent rights licensed to BMS under this Agreement. UM shall have the right to assume and control the defense and settlement of any such UM Liabilities, and BMS shall reasonably cooperate in those activities. For clarity, this indemnity shall apply even if UM were to default in making any required payments to a Third Party (including HHMI). UM’s obligation under this Section 6.3 shall terminate if this Agreement is terminated under Section 7.3. This Section 6.3 shall not be subject to Section 5.5.

ARTICLE 7

TERM AND TERMINATION

7.1 Term. This Agreement shall commence as of the Effective Date and, unless sooner terminated in accordance with this Article 7, shall continue thereafter in accordance with its terms and conditions.

7.2 Termination By BMS. Subject to Section 7.4, BMS shall have the right to terminate this Agreement upon delivery of written notice to Licensors in the event of any material breach by Repligen and/or UM of any terms and conditions of this Agreement, provided that such breach has not been cured within ninety (90) business days after written notice thereof is given by BMS to Licensors specifying the nature of the alleged breach.

7.3 Termination By Repligen. Subject to Section 7.4, Repligen shall have the right to terminate this Agreement upon delivery of written notice to BMS in the event of any material breach by

BMS of any terms and conditions of this Agreement, provided that such breach has not been cured within ninety (90) business days after written notice thereof is given by Repligen to BMS specifying the nature of the alleged breach.

7.4 Disputed Breach. If a Party disputes in good faith the existence or materiality of a breach specified in a notice provided under Section 7.2 or 7.3, the Party providing such notice shall not have the right to terminate this Agreement unless and until such dispute has been resolved (including as necessary through litigation). It is understood and acknowledged that during the pendency of such a dispute, all of the terms and conditions of this Agreement shall remain in full force and effect.

7.5 Effect of Termination. Termination or expiration of this Agreement shall not relieve the Parties of any liability or obligation which accrued hereunder prior to the effective date of such termination or expiration nor preclude either Party from pursuing all rights and remedies it may have hereunder or at law or in equity, with respect to any breach of this Agreement nor prejudice either Party’s right to obtain performance of any obligation. Termination of this Agreement in whole or in part for any reason shall not relieve BMS of its obligations to pay all royalties that shall have accrued hereunder prior to the effective date of termination. Subject to and without limiting BMS’s rights under the first sentence of this Section 7.5, termination of this Agreement shall result in the termination of the licenses and covenants granted to BMS and its Sublicensees under Article 2, except as provided in Section 7.6. The provisions of Section 4.4, Article 5, Article 6, and Sections 7.5, 7.6, 9.4, 9.8 and 9.13 shall survive termination of the Agreement for any reason.

7.6 Direct License to Sublicensee on Termination. A sublicense granted by BMS to a Sublicensee under this Agreement shall survive termination of this Agreement and shall be deemed to be a direct license from each Licensor to such Sublicensee beginning on the date of termination, provided that (i) such Sublicensee is then in full compliance with all terms of this Agreement and the respective sublicense, (ii) BMS is then in full compliance with all terms of this Agreement, including but not limited to Section 2.2, with respect to such sublicense, (iii) such Sublicensee agrees in writing to assume all of the obligations of BMS under this Agreement and can reasonably show the capacity to comply with such obligations to the same extent as BMS, (iv) the obligations of Licensor under such direct license shall not be greater than the obligations of Licensor under this Agreement, (v) the scope of such direct license shall not be broader than the rights sublicensed by BMS to such Sublicensee and (vi) no Licensor shall accept any liability with respect to such sublicense incurred prior such date of termination.

ARTICLE 8

PATENT PROSECUTION AND ENFORCEMENT

8.1 Prosecution and Maintenance of the Thompson Patents Rights. Subject to Section 8.2 and without limiting any rights of BMS that may exist separately from this Agreement, the Licensors retain control of Prosecution and Maintenance of Licensed Patents, and agree to maintain any issued patent within the Thompson Patent Rights at the expense of the Licensors by timely paying any applicable government imposed maintenance fees. Any costs associated with Prosecution and Maintenance of applications within the Licensed Patents shall be borne by the Licensors, except as provided in Section 8.2. Notwithstanding the foregoing, the Parties agree that Licensors will abandon the following applications:

U.S. Serial No. 12/044,679; JP 2006-284411; CA 2,133,075; and EP 4015607.7 (published as EP1488805A).

8.2 Transfer of Prosecution and Maintenance of Licensed Patents. If a Licensor elects not to continue Prosecution and Maintenance of any patents or patent applications within Thompson Patent Rights (other than U.S. Serial No. 12/044,679; JP 2006-284411; CA 2,133,075; and EP 4015607.7 (published as EP1488805A)) for which Prosecution and Maintenance is controlled by it (the “Transferring Party”), that Party shall notify BMS in writing of such election at least thirty (30) days prior to the last available date for action to preserve such patents or patent applications. At BMS’s option, BMS can elect to continue Prosecution and Maintenance of such patents or patent applications at its sole expense. In such case, the Transferring Party will provide BMS with all reasonable assistance and cooperation, and execute such documents, as are necessary to continue or permit continuing Prosecution and Maintenance of such patents or patent applications by BMS, including, but not limited to, make its employees and agents reasonably available to BMS (or to BMS’s authorized attorneys, agents or representatives) to the extent reasonably necessary to enable BMS to continue Prosecution and Maintenance of such patents or patent applications.

8.3 Liability. Upon assuming Prosecution and Maintenance of a patent or patent application under Section 8.2, BMS will have no liability with regard to Prosecution and Maintenance assumed by it, and will be free, at its sole option, to discontinue Prosecution and Maintenance of such patent or patent application at any time without further notification to or approval by the Transferring Party or other Party under this Agreement.

8.4 Status Reports. At BMS’s reasonable request, each Licensor agrees to provide, for any or all Licensed Patents for which Prosecution and Maintenance is being conducted by or on behalf of such Licensor: (1) a status report (including, but not limited to, the country, application or patent number, and status (such as pending, granted, or expired)) for such Licensed Patents, and (2) copies of all material correspondence after the Effective Date of this Agreement with the U.S. Patent and Trademark Office (“USPTO”) or its foreign counterparts for such Licensed Patents, to the extent that such correspondence is not otherwise publicly available and to the extent that BMS does not already possess such copies. Licensors agree to negotiate with BMS in good faith to provide that any material correspondence with the USPTO or its foreign counterparts for such Licensed Patents shall not be subject to any further obligations of Paragraph 24 of the Parties’ “Protective Order” filed March 8, 2007.

8.5 Enforcement of the Licensed Patents. BMS shall have the first opportunity in its sole discretion, but not the obligation, to enforce the Thompson Patent Rights at its expense. Licensors agree to reasonably assist BMS, upon BMS’s request and at BMS’s expense, in taking action to enforce the Thompson Patent Rights. Licensors will join any such action as parties if requested by BMS, at BMS’s expense if they are represented by BMS’s counsel, otherwise at their own expense. All monies recovered upon the final judgment or settlement of any such action, to the extent based on the enforcement of the Thompson Patent Rights, shall be used first, to reimburse the costs and expenses (including reasonable attorneys’ fees and costs) of the Parties with respect to such action, with the remainder to be divided as follows: (i) as to ordinary damages based on lost sales or profits, BMS shall retain such funds and such funds based on lost sales or profits during the Royalty Term will be treated as Net Sales and royalties will be payable by BMS to Repligen with respect to such Net Sales in accordance with this Agreement and (ii) as to special or punitive damages, BMS shall retain such damages. In no event shall BMS have any obligation to join any action brought to enforce the Thompson Patent Rights.

ARTICLE 9

MISCELLANEOUS PROVISIONS

9.1 Relationship of the Parties. Nothing in this Agreement is intended or shall be deemed to constitute or give rise to a partnership, agency, distributorship, employer-employee, joint venture, or

fiduciary relationship between the Parties. No Party shall incur any debts or make any commitments for the other.

9.2 Assignment. This Agreement may not be assigned or otherwise transferred by a Party without the consent of the other Parties which consent shall not be unreasonably withheld; provided however, that BMS, UM or Repligen may, without such consent, assign this Agreement together with all of its rights and obligations hereunder to its Affiliates, or to a successor in interest in connection with the transfer or sale of all or substantially all of its business to which this Agreement relates, or in the event of its merger or consolidation or change in control or similar transaction, subject in each such case to the assignee agreeing to be bound by the terms of this Agreement, including without limitation the obligations and covenants under Section 2.3 and 2.4. Any permitted assignee of any of the Licensed Patents shall agree to be bound by all applicable terms of this Agreement, including without limitation the obligations and covenants under Section 2.3 and 2.4. Any permitted assignee or successor shall assume and be bound by all obligations of its assignor or predecessor under this Agreement. Any purported assignment in violation of the preceding sentences in this Section 9.2 shall be void.

9.3 Further Acts and Instruments. Upon request by a Party, the other Party(ies) agrees to execute, acknowledge and deliver such further instruments, and to do all such other acts, as may be reasonably necessary or appropriate in order to carry out the purposes and intent of this Agreement.

9.4 Use of Names and Trademarks. Except as otherwise provided herein, no right, expressed or implied, is granted by this Agreement to use in any commercial manner the name of a Party, Navy, HHMI, Craig B. Thompson, or Carl H. June or any other trade name or trademark of such entities or individuals in connection with the performance of this Agreement. Subject to any other limitations of this Agreement, this Section 9.4 shall not prohibit a Party from disclosing the name of a Party solely in the public reporting of this Agreement.

9.5 Entire Agreement. This Agreement, together with its Exhibits, constitutes and contains the entire understanding and agreement of the Parties with respect to the subject matter hereof, and cancels and supersedes any and all prior negotiations, correspondence, understandings and agreements, whether verbal or written, between the Parties respecting the subject matter hereof, including but not limited to the term sheet executed by the Parties on March 4, 2008. No waiver, modification, or amendment of any provision of this Agreement shall be valid or effective unless made in writing and signed by a duly authorized representative of each of the Parties.

9.6 Severability. In the event any one or more of the provisions of this Agreement should for any reason be held by any court or authority having jurisdiction over this Agreement or either of the Parties to be invalid, illegal or unenforceable, such provision or provisions shall be validly reformed to as nearly as possible approximate the intent of the Parties and, if unreformable, shall be divisible and deleted in such jurisdiction; elsewhere, this Agreement shall not be affected so long as the Parties are still able to realize the principal benefits bargained for in this Agreement.

9.7 Waiver. The waiver by a Party of any breach of or default under any of the provisions of this Agreement or the failure of a Party to enforce any of the provisions of this Agreement or to exercise any right hereunder shall not constitute or be construed as a waiver of any other breach or default or as a waiver of any such rights or provisions hereunder.

9.8 Governing Law. This Agreement shall be governed by, enforced, and shall be construed in accordance with the laws of the State of Delaware without regard to its conflicts of law provisions. For the purposes of any suit, action or other proceeding arising out of, or under or in connection with this Agreement, the Parties are free to agree or not agree to the form of such proceeding, whether litigation or

arbitration, provided that, in the event that any suit, action or other proceeding is to be submitted to a court (whether as agreed upon by all Parties or, in the absence of an agreement, through any one of them), the Parties hereby will irrevocably submit to the jurisdiction of (i) the United States District Court for the Eastern District of Texas or the United States District Court for the District of Delaware (each a “District Court”), and otherwise to the exclusive jurisdiction of (ii) the Supreme Court or Chancery Court of the State of Delaware (each a “State Court”) . Each Party agrees to commence any such action, suit or proceeding in such District Court or if such suit, action or other proceeding may not be brought in such court for jurisdictional reasons, in a State Court. Each Party further agrees that service of any process, summons, notice or document by certified mail, return receipt requested, to such Party’s respective address set forth below in Section 9.9 shall be effective service of process for any action, suit or other proceeding with respect to any matters to which it has submitted to jurisdiction in this Section. Each Party irrevocably and unconditionally waives any defense or objection to the laying of venue of any action, suit or other proceeding arising out of this Agreement in (i) a State Court, or (ii) the District Court, and hereby and thereby further irrevocably and unconditionally waives and agrees not to plead or claim any defense or objection in any such court that any such action, suit or other proceeding brought in any such court has been brought in an inconvenient forum.

9.9 Notices. Any notice, request, consent, or other document required or permitted to be given under this Agreement or otherwise relating to this Agreement shall be in writing and shall be deemed to have been sufficiently given if delivered in person, transmitted by facsimile (with a confirming copy sent by overnight courier), or sent by overnight courier or registered mail to the Party to whom it is directed at its address shown below or such other address as such Party shall have last given by notice to the other Party. Any such notice, requests, delivery, approval or consent shall be deemed received on the date of hand delivery or transmission by facsimile (provided that such date is a business day, otherwise it shall be deemed received on the next business day), one (1) business day after dispatch by overnight courier, or five (5) business days after dispatch of the registered mail. The Parties may agree by written or electronic acknowledgment on a case-by-case basis to accept such notice, request, consent, or other document by other means, such as electronic transmission.

If to BMS, addressed to:

Bristol-Myers Squibb Company

P.O. Box 4000

Route 206 & Province Line Road

Princeton, NJ 08543-4000

Attention: Senior Vice President, Corporate and Business Development

With a copy to:

Bristol-Myers Squibb Company

P.O. Box 4000

Route 206 & Province Line Road

Princeton, NJ 08543-4000

Attention: Vice President & Senior Counsel, Business Development

If to Repligen, addressed to:

Repligen Corporation

41 Seyon Street

Building #1, Suite 100

Waltham, MA 02453

Attention: President and Chief Executive Officer

If to UM, addressed to:

University of Michigan

Office of Technology Transfer

1214 S. University Ave., 2^nd Floor

Ann Arbor, MI 48104-2592

9.10 Press Release. Upon execution of this Agreement, Repligen shall issue a press release announcing this Agreement in the mutually agreed upon form attached hereto as Exhibit B.

9.11 Bankruptcy. The Parties agree that in the event a Party becomes a debtor under Title 11 of the U.S. Code (“Title 11”), this Agreement shall be deemed to be, for purposes of Section 365(n) of Title 11, a license to rights to “intellectual property” as defined therein. Each Party as a licensee hereunder shall have the rights and elections as specified in Title 11. Any agreements supplemental hereto shall be deemed to be “agreements supplementary to” this Agreement for purposes of Section 365(n) of Title 11.

9.12 Dispute Resolution. The Parties shall seek to settle amicably any and all disputes or claims arising out of or in connection with this Agreement. Any such dispute or claim between the Parties shall be presented to senior representatives of each Party (to be designated by each Party) (such representatives of each Party being the “Senior Representatives”) for resolution. Such Senior Representatives, or their respective designees, will meet in-person or by teleconference as soon as reasonably possible thereafter, and use their good faith efforts to mutually agree upon the resolution of the dispute or claim. If such dispute or claim cannot be resolved within sixty (60) days of presentation to the Senior Representatives, or their respective designees, for resolution, unless the Parties otherwise agree in writing, any Party may pursue the resolution of such dispute or claim through litigation in accordance with Section 9.8.

9.13 Interpretation.

(a) Each of the Parties acknowledges and agrees that this Agreement has been diligently reviewed by and negotiated by and between them, that in such negotiations each of them has been represented by competent counsel and that the final agreement contained herein, including the language whereby it has been expressed, represents the joint efforts of the Parties hereto and their counsel. Accordingly, in interpreting this Agreement or any provision hereof, no presumption shall apply against any Party hereto as being responsible for the wording or drafting of this Agreement or any such provision, and ambiguities, if any, in this Agreement shall not be construed against any Party, irrespective of which Party may be deemed to have authored the ambiguous provision.

(b) The definitions of the terms herein shall apply equally to the singular and plural forms of the terms defined. Whenever the context may require, any pronoun shall include the corresponding masculine, feminine and neuter forms. The words “include”, “includes” and “including” shall be deemed to be followed by the phrase “without limitation”. The word “will” shall be construed to have the same meaning and effect as the word “shall”. The word “any” shall mean “any and all” unless otherwise clearly indicated by context.

(c) Unless the context requires otherwise, (i) 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 amendments, supplements or modifications set forth herein or therein), (ii) any reference to any laws herein shall be construed as referring to such laws as from time to time enacted, repealed or amended, (iii) any reference herein to any Person shall be construed to include the Person’s successors and assigns, (iv) 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, and (v) all references herein to Articles or Sections, unless otherwise specifically provided, shall be construed to refer to Articles and Sections of this Agreement.

(d) Headings and captions are for convenience only and are not be used in the interpretation of this Agreement.

9.14 Counterparts. This Agreement may be executed simultaneously in three or more counterparts, any one of which need not contain the signature of more than one party, but all such counterparts taken together shall constitute one and the same instrument, and may be executed and delivered through the use of facsimiles or email of pdf copies of the executed Agreement.

* * *

[signature page follows]

IN WITNESS WHEREOF, Licensors and BMS have caused this Agreement to be executed by their duly authorized representatives.

REPLIGEN CORPORATION

By:

Title:

Date:

THE REGENTS OF THE UNIVERSITY OF MICHIGAN

By:

Title:

Date:

BRISTOL-MYERS SQUIBB COMPANY

By:

Title:

Date:

EXHIBIT A

IN THE UNITED STATES DISTRICT COURT

FOR THE EASTERN DISTRICT OF TEXAS

MARSHALL DIVISION

REPLIGEN CORPORATION and THE REGENTS OF THE UNIVERSITY OF MICHIGAN,   Plaintiffs,                   v.   BRISTOL-MYERS SQUIBB COMPANY,   Defendant. Case No. 2:06-cv-4-TJW

STIPULATION OF DISMISSAL

WHEREAS Plaintiffs Repligen Corporation and The Regents of the University of Michigan (collectively “Plaintiffs”) and Defendant Bristol-Myers Squibb Company (“Bristol”), as indicated by the signature of counsel appearing below, have agreed to the dismissal of this action, pursuant to Federal Rule of Civil Procedure 41 and subject to the terms of this Order and a settlement agreement, dated April __, 2008,

NOW, THEREFORE, it is ordered as follows:

1. The claims by Plaintiffs against Bristol are hereby dismissed with prejudice.

2. The claims by Bristol against Plaintiffs are hereby dismissed with prejudice.

3. Each party shall bear its own costs and attorneys fees attributable to the prosecution and defense of the claims.

STIPULATED AND AGREED

BY:		BY:
	Samuel F. Baxter (Bar No. 01938000) McKOOL SMITH P.C. 505 East Travis Street, Suite 105 Marshall, Texas 75670 (903) 927-2111 (903) 927-2622 (facsimile) OF COUNSEL: John Garvish (Bar No. 24043681) McKOOL SMITH P.C. 300 W. 6th Street, Suite 1700 Austin TX 78701 (512) 692.8731 (512) 692.8744 Ahmed J. Davis FISH & RICHARDSON P.C. 1425 K Street, N.W., 11th Floor Washington, DC 20005 (202) 783-5070 (202) 783-2331 (facsimile) Juanita Brooks FISH & RICHARDSON P.C. 12390 El Camino Real San Diego, CA 92130 (858) 678-5070 (858) 678-5099 (facsimile) Robert E. Hillman Ramon Tabtiang Stephen A. Marshall		Robert L. Baechtold Lead Attorney for Defendant Bristol-Myers Squibb Company FITZPATRICK CELLA HARPER & SCINTO 30 Rockefeller Plaza New York, N.Y. 10112 Telephone: (212) 218-2100 Facsimile: (212) 218-2200 rbaechtold@fchs.com OF COUNSEL: Scott K. Reed sreed@fchs.com Colleen Tracy ctracy@fchs.com Christopher P. Borello cborello@fchs.com FITZPATRICK CELLA HARPER & SCINTO 30 Rockefeller Plaza New York, N.Y. 10112 Telephone: (212) 218-2100 Facsimile: (212) 218-2200 J. Wesley Hill Texas Bar No. 24032294 IRELAND CARROLL & KELLEY, P.C. 6101 South Broadway Tyler, Texas 75703 Telephone: (903) 561-1600 Facsimile: (903) 581-1071 wesleyhill@icklaw.com
	FISH & RICHARDSON P.C.	Attorneys For Defendant, BRISTOL-MYERS SQUIBB
	225 Franklin Street	COMPANY
	Boston, MA 02110
	(617) 542-5070
	(617) 542-8906 (facsimile)
Attorneys For Plaintiffs REPLIGEN CORPORATION and REGENTS OF THE UNIVERSITY OF MICHIGAN
SO ORDERED this              day of                             , 2008.

Honorable T. John Ward

EXHIBIT B

Press Release

	Repligen Corporation
	41 Seyon Street
RepliGen	Building #1, Suite 100
	Waltham, Massachusetts 02453
	Telephone: 781-250-0111
FOR IMMEDIATE RELEASE	Telefax: 781-250-0115

CONTACT:

Walter C. Herlihy, Ph.D. President and Chief Executive Officer (781) 419-1900 Laura Whitehouse Vice President, Market Development (781) 419-1812

Repligen Announces Settlement with Bristol-Myers Squibb in Orencia^®

Lawsuit

WALTHAM, MA – April      , 2008 – Repligen Corporation (NASDAQ: RGEN) announced today that it has reached a settlement with Bristol-Myers Squibb Company (NYSE: BMY) in its lawsuit alleging infringement of U.S. Patent No. 6,685,941 (“the ‘941 patent”), based on Bristol-Myers Squibb’s sale of Orencia^® for the treatment of rheumatoid arthritis. The settlement provides for Bristol-Myers Squibb to make an initial payment of $5,000,000 and to pay royalties on the 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 U.S. annual sales in excess of $1 billion for each year from January 1, 2008 until December 31, 2013. The settlement also provides for the grant by Repligen and co-plaintiff the University of Michigan to Bristol-Myers Squibb of an exclusive worldwide license under certain patent rights of Repligen and the University of Michigan. The settlement serves as the basis for Repligen and co-plaintiff the University of Michigan to dismiss the lawsuit against Bristol-Myers Squibb.

“We are very pleased by the settlement of this case which will provide us a substantial new source of revenue,” stated Walter C. Herlihy, President and Chief Executive Officer of Repligen Corporation. “Based on analysts’ estimates of U.S. sales of Orencia^®, we expect total cash receipts from our Protein A business, Orencia^® royalties, research and development and other income of greater than $30 million for fiscal year 2009, beginning April 1, 2008.”

In January 2006, Repligen and the University of Michigan filed a complaint in the United States District Court for the Eastern District of Texas against Bristol-Myers Squibb alleging infringement of the ‘941 patent based on its sale of Orencia^®. The claims of the ‘941 patent relate to the use of CTLA4-Ig (Orencia^®) for the treatment of specific auto-immune diseases, including rheumatoid arthritis. The ‘941 patent is owned by the University of Michigan and the United States Department of the Navy and is exclusively licensed to Repligen.

About Repligen Corporation

Repligen Corporation is a biopharmaceutical company focused on the development of novel therapeutics for diseases that affect the central nervous system. In addition, we are the world’s leading supplier of recombinant Protein A, the sales of which partially fund the advancement of our development pipeline while supporting our financial stability. Repligen’s corporate headquarters are located at 41 Seyon Street, Building #1, Suite 100, Waltham, MA 02453. Additional information may be requested from 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. The forward-looking statements in this release do not constitute guarantees of future performance. Investors are cautioned that statements in this press release which are not strictly historical statements, including, without limitation, statements regarding current or future financial performance and position, management’s strategy, plans and objectives for future operations, plans and objectives for product development, plans and objectives for present and future clinical trials and results of such trials, plans and objectives for regulatory approval, litigation, intellectual property, product development, manufacturing plans and performance such as the anticipated growth in the monoclonal antibody market and our other target markets and projected growth in product sales, 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 current and future collaborative relationships, the market acceptance of our products, our ability to compete with larger, better financed pharmaceutical and biotechnology companies, new approaches to the treatment of our targeted diseases, our expectation of incurring continued losses, our uncertainty of product revenues and profits, our ability to generate future revenues, our ability to raise additional capital to continue our drug development programs, the success of our clinical trials, our ability to develop and commercialize products, our ability to obtain required regulatory approvals, our compliance with all Food and Drug Administration 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 and manufacturing capabilities, our dependence on third-party manufacturers and value added resellers, our ability to hire and retain skilled personnel, our volatile stock price, and other risks detailed in Repligen’s filings with the Securities and Exchange Commission. Repligen assumes no obligation to update any forward-looking information contained in this press release or with respect to the announcements described herein.

EX-31.1

Exhibit 31.1

CERTIFICATION

I, Walter Herlihy, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q 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 registrant’s board of directors (or persons performing the equivalent function):

(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: August 8, 2008

/s/ Walter C. Herlihy

Walter C. Herlihy

Chief Executive Officer and President

(Principal Executive Officer)

EX-31.2

Exhibit 31.2

CERTIFICATION

I, William Kelly, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q 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 registrant’s board of directors (or persons performing the equivalent function):

(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: August 8, 2008

/s/ William J. Kelly

William J. Kelly

Vice President Finance and Administration

(Principal Financial and Accounting 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 Quarterly Report of Repligen Corporation (the “Company”) on Form 10-Q for the period ending June 30, 2008 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 the undersigneds’ 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 result of operations of the Company.

Date: August 8, 2008	By:	/s/ Walter C. Herlihy
		Walter C. Herlihy
		Chief Executive Officer and President
		(Principal Executive Officer)
Date: August 8, 2008	By:	/s/ William J. Kelly
		William J. Kelly
		Vice President, Finance and Administration
		(Principal Financial and Accounting Officer)