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 March 31, 2013
OR
o	TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the transition period from              to
Commission File Number 000-50513

ACORDA THERAPEUTICS, INC.

(Exact name of registrant as specified in its charter)

  Delaware (State or other jurisdiction of incorporation or organization) 13-3831168 (I.R.S. Employer Identification No.)

420 Saw Mill River Road, Ardsley, New York (Address of principal executive offices) 10502 (Zip Code)

(914) 347-4300

(Registrant’s telephone number,

including area code)

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 o

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

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

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

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

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date.

Class	Outstanding at April 30, 2013
Common Stock, $0.001 par value per share	40,566,088 shares

ACORDA THERAPEUTICS, INC.

TABLE OF CONTENTS

		Page
PART I—FINANCIAL INFORMATION
Item 1.	Financial Statements	1
	Consolidated Balance Sheets March 31, 2013 (unaudited) and December 31, 2012	1
	Consolidated Statements of Operations (unaudited) Three-month Period Ended March 31, 2013 and 2012	2
	Consolidated Statements of Comprehensive (Loss) Income (unaudited) Three-month Period Ended March 31, 2013 and 2012	3
	Consolidated Statements of Cash Flows (unaudited) Three-month period ended March 31, 2013 and 2012	4
	Notes to Consolidated Financial Statements (unaudited)	5
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	15
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	26
Item 4.	Controls and Procedures	26
PART II—OTHER INFORMATION
Item 1.	Legal Proceedings	27
Item 1A.	Risk Factors	27
Item 6.	Exhibits	27

This Quarterly Report on Form 10-Q contains forward-looking statements relating to future events and our future performance within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. Stockholders are cautioned that such statements involve risks and uncertainties, including:  our ability to successfully market and sell Ampyra in the U.S.; third party payers (including governmental agencies) may not reimburse for the use of Ampyra or our other products at acceptable rates or at all and may impose restrictive prior authorization requirements that limit or block prescriptions; the risk of unfavorable results from future studies of Ampyra or from our other research and development programs, including Diazepam Nasal Spray or any other acquired or in-licensed programs; we may not be able to complete development of, obtain regulatory approval for, or successfully market Diazepam Nasal Spray or other products under development; the occurrence of adverse safety events with our products; delays in obtaining or failure to obtain regulatory approval of or to successfully market Fampyra outside of the U.S. and our dependence on our collaboration partner Biogen Idec in connection therewith; competition, including the impact of generic competition on Zanaflex Capsules revenues; failure to protect our intellectual property, to defend against the intellectual property claims of others, or to obtain third party intellectual property licenses needed for the commercialization of our products; failure to comply with regulatory requirements could result in adverse action by regulatory agencies; and the ability to obtain additional financing to support our operations. These forward-looking statements are based on current expectations, estimates, forecasts and projections about the industry and markets in which we operate and management’s beliefs and assumptions. All statements, other than statements of historical facts, included in this report regarding our strategy, future operations, future financial position, future revenues, projected costs, prospects, plans and objectives of management are forward-looking statements. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would,” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make, and investors should not place undue reliance on these statements. In addition to the risks and uncertainties described above, we have included important factors in the cautionary statements included in this report and in our Annual Report on Form 10-K for the year ended December 31, 2012, particularly in the “Risk Factors” section, that we believe could cause actual results or events to differ materially from the forward-looking statements that we make. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments that we may make. Forward-looking statements in this report are made only as of the date hereof, and we do not assume any obligation to publicly update any forward-looking statements as a result of developments occurring after the date of this report.

We own several registered trademarks in the U.S. and in other countries.  These registered trademarks include, in the U.S., the marks “Acorda Therapeutics,” our stylized Acorda Therapeutics logo, “Ampyra,” “Zanaflex,” and “Zanaflex Capsules.”  Also, our mark “Fampyra” is a registered mark in the European Community Trademark Office and we have registrations or pending applications for this mark in other jurisdictions.  Our trademark portfolio also includes several registered trademarks and pending trademark applications in the U.S. and worldwide for potential product names or for disease awareness activities.  Third party trademarks, trade names, and service marks used in this report are the property of their respective owners.

PART I

Item 1.  Financial Statements

ACORDA THERAPEUTICS, INC. AND SUBSIDIARIES

Consolidated Balance Sheets

(In thousands, except share data)	March 31,  2013			December 31, 2012
	(unaudited)
Assets
Current assets:
Cash and cash equivalents	$	34,687		$	41,876
Restricted cash		34			380
Short-term investments		248,659			191,949
Trade accounts receivable, net of allowances of $587 and $555, as of March 31, 2013 and December 31, 2012, respectively		23,288			26,327
Prepaid expenses		7,606			6,936
Finished goods inventory held by the Company		27,850			20,176
Finished goods inventory held by others		736			781
Deferred tax asset		36,955			35,091
Other current assets		11,060			9,547
Total current assets		390,875			333,063
Long-term investments		41,559			99,363
Property and equipment, net of accumulated depreciation		16,936			16,706
Deferred tax asset		101,545			101,636
Intangible assets, net of accumulated amortization		9,446			9,319
Non-current portion of deferred cost of license revenue		4,649			4,808
Other assets		413			437
Total assets	$	565,423		$	565,332
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	24,077		$	22,503
Accrued expenses and other current liabilities		31,786			35,758
Deferred product revenue—Zanaflex		29,620			29,275
Current portion of deferred license revenue		9,057			9,057
Current portion of revenue interest liability		1,180			1,134
Current portion of convertible notes payable		1,144			1,144
Total current liabilities		96,864			98,871
Non-current portion of deferred license revenue		66,421			68,685
Put/call liability		247			329
Non-current portion of revenue interest liability		891			1,111
Non-current portion of convertible notes payable		3,133			4,244
Other non-current liabilities		6,228			6,171
Commitments and contingencies
Stockholders’ equity:
Common stock, $0.001 par value. Authorized 80,000,000 shares at March 31, 2013 and December 31, 2012; issued and outstanding 39,893,408 and 39,804,493 shares, including those held in treasury, as of March 31, 2013 and December 31, 2012, respectively		40			40
Treasury stock at cost (12,420 shares at March 31, 2013 and December 31, 2012)		(329	)		(329	)
Additional paid-in capital		647,507			640,671
Accumulated deficit		(255,662	)		(254,523	)
Accumulated other comprehensive income		83			62
Total stockholders’ equity		391,639			385,921
Total liabilities and stockholders’ equity	$	565,423		$	565,332

See accompanying Unaudited Notes to Consolidated Financial Statements

1

ACORDA THERAPEUTICS, INC. AND SUBSIDIARIES

Consolidated Statements of Operations

(unaudited)

(In thousands, except per share data)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Revenues:
Net product revenues	$	64,084		$	65,673
Royalty revenues		5,516			3,310
License revenue		2,265			2,265
Total net revenues		71,865			71,248
Costs and expenses:
Cost of sales		13,484			12,464
Cost of license revenue		159			159
Research and development		12,520			11,025
Selling, general and administrative		48,198			38,745
Total operating expenses		74,361			62,393
Operating (loss) income		(2,496	)		8,855
Other expense (net):
Interest and amortization of debt discount expense		(591	)		(766	)
Interest income		173			129
Total other expense (net)		(418	)		(637	)
(Loss) income before taxes		(2,914	)		8,218
Benefit from (provision for) income taxes		1,775			(372	)
Net (loss) income	$	(1,139	)	$	7,846
Net (loss) income per share—basic	$	(0.03	)	$	0.20
Net (loss) income per share—diluted	$	(0.03	)	$	0.19
Weighted average common shares outstanding used in computing net (loss) income per share—basic		39,832			39,340
Weighted average common shares outstanding used in computing net (loss) income per share—diluted		39,832			40,407

See accompanying Unaudited Notes to Consolidated Financial Statements

2

ACORDA THERAPEUTICS, INC. AND SUBSIDIARIES

Consolidated Statements of Comprehensive (Loss) Income

(unaudited)

(In thousands)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Net (loss) income	$	(1,139	)	$	7,846
Other comprehensive income (loss):
Unrealized gains (losses) on available for sale securities, net of tax		21			(100	)
Other comprehensive income (loss), net of tax		21			(100	)
Comprehensive (loss) income	$	(1,118	)	$	7,746

See accompanying Unaudited Notes to Consolidated Financial Statements

3

ACORDA THERAPEUTICS, INC. AND SUBSIDIARIES

Consolidated Statements of Cash Flows

(unaudited)

(In thousands)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Cash flows from operating activities:
Net (loss) income	$	(1,139	)	$	7,846
Adjustments to reconcile net income to net cash provided by operating activities:
Share-based compensation expense		4,933			4,191
Amortization of net premiums and discounts on investments		586			1,507
Amortization of revenue interest issuance cost		16			30
Depreciation and amortization expense		1,400			912
Gain on put/call liability		(82	)		(535	)
Deferred tax benefit		(1,772	)		—
Changes in assets and liabilities:
Decrease in accounts receivable		3,039			1,302
Increase in prepaid expenses and other current assets		(2,183	)		(5,459	)
Increase in inventory held by the Company		(7,674	)		(357	)
Decrease in inventory held by others		45			81
Decrease in non-current portion of deferred cost of license revenue		159			159
Decrease (increase) in other assets		8			(92	)
Decrease in accounts payable, accrued expenses, other current liabilities		(3,510	)		(6,144	)
Increase in revenue interest liability interest payable		92			421
Decrease in non-current portion of deferred license revenue		(2,264	)		(2,264	)
Increase in other non-current liabilities		—			1,858
Increase (decrease) in deferred product revenue—Zanaflex		345			(444	)
Decrease in restricted cash		346			—
Net cash (used in) provided by operating activities		(7,655	)		3,012
Cash flows from investing activities:
Purchases of property and equipment		(1,060	)		(3,104	)
Purchases of intangible assets		(641	)		(656	)
Purchases of investments		(27,471	)		(65,396	)
Proceeds from maturities of investments		28,000			61,750
Net cash used in investing activities		(1,172	)		(7,406	)
Cash flows from financing activities:
Proceeds from issuance of common stock and option exercises		1,903			1,949
Repayments of revenue interest liability		(265	)		(209	)
Net cash provided by financing activities		1,638			1,740
Net decrease in cash and cash equivalents		(7,189	)		(2,654	)
Cash and cash equivalents at beginning of period		41,876			57,954
Cash and cash equivalents at end of period	$	34,687		$	55,300
Supplemental disclosure:
Cash paid for interest		466			304
Cash paid for taxes		731			165

See accompanying Unaudited Notes to Consolidated Financial Statements

4

ACORDA THERAPEUTICS, INC. AND SUBSIDIARIES

Notes to Consolidated Financial Statements

(unaudited)

(1) Organization and Business Activities

Acorda Therapeutics, Inc. (“Acorda” or the “Company”) is a commercial stage biopharmaceutical company dedicated to the identification, development and commercialization of novel therapies that improve neurological function in people with multiple sclerosis (MS), spinal cord injury (SCI) and other disorders of the central nervous system.

The management of the Company is responsible for the accompanying unaudited interim consolidated financial statements and the related information included in the notes to the consolidated financial statements. In the opinion of management, the unaudited interim consolidated financial statements reflect all adjustments, including normal recurring adjustments necessary for the fair presentation of the Company’s financial position and results of operations and cash flows for the periods presented. Results of operations for interim periods are not necessarily indicative of the results to be expected for the entire year.

These unaudited interim consolidated financial statements should be read in conjunction with the audited consolidated financial statements of the Company as of and for the year ended December 31, 2012 included in the Company’s Annual Report on Form 10-K for such year, as filed with the Securities and Exchange Commission (the “SEC”).

 (2) Summary of Significant Accounting Policies

Principles of Consolidation

The accompanying consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States of America and include the results of operations of the Company and its majority owned subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of the consolidated financial statements requires management of the Company to make a number of estimates and assumptions relating to the reported amount of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the period. Significant items subject to such estimates and assumptions include share-based compensation accounting, which are largely dependent on the fair value of the Company’s equity securities. In addition, the Company recognizes Zanaflex revenue based on estimated prescriptions filled. The Company adjusts its Zanaflex inventory value based on an estimate of inventory that may be returned. Actual results could differ from those estimates.

Investments

Both short-term and long-term investments consist of US Treasury bonds. The Company classifies marketable securities available to fund current operations as short-term investments in current assets on its consolidated balance sheets. Marketable securities are classified as long-term investments in long-term assets on the consolidated balance sheets if the Company has the ability and intent to hold them and such holding period is longer than one year. The Company classifies its short-term and long-term investments as available-for-sale. Available-for-sale securities are recorded at fair value of the investments based on quoted market prices.

Unrealized holding gains and losses on available-for-sale securities, which are determined to be temporary, are excluded from earnings and are reported as a separate component of accumulated other comprehensive income (loss).

Premiums and discounts on investments are amortized over the life of the related available-for-sale security as an adjustment to yield using the effective-interest method. Dividend and interest income are recognized when earned. Amortized premiums and discounts, dividend and interest income and realized gains and losses are included in interest income.

5

Accumulated Other Comprehensive Income

The Company’s accumulated other comprehensive income is comprised of gains and losses on available for sale securities and is recorded and presented net of income tax.

Revenue Recognition

Ampyra

Ampyra is available only through a network of specialty pharmacy providers that provide the medication to patients by mail; Kaiser Permanente (Kaiser), which distributes Ampyra to patients through a closed network of on-site pharmacies; and ASD Specialty Healthcare, Inc. (an AmerisourceBergen affiliate), which is the exclusive specialty pharmacy distributor for Ampyra to the U.S. Bureau of Prisons and the U.S. Department of Veterans Affairs (VA). Ampyra is not available in retail pharmacies. The Company does not recognize revenue from product sales until there is persuasive evidence of an arrangement, delivery has occurred, the price is fixed and determinable, the buyer is obligated to pay the Company, the obligation to pay is not contingent on resale of the product, the buyer has economic substance apart from the Company, the Company has no obligation to bring about the sale of the product, and the amount of returns can be reasonably estimated and collectability is reasonably assured. The Company recognizes product sales of Ampyra following shipment of product to a network of specialty pharmacy providers, Kaiser, and the specialty distributor to the VA. The specialty pharmacy providers, Kaiser, and the specialty distributor to the VA are contractually obligated to hold no more than an agreed number of days of inventory, ranging from 10 to 30 days.

The Company’s net revenues represent total revenues less allowances for customer credits, including estimated rebates, discounts and returns. These allowances are recorded for cash consideration given by a vendor to a customer that is presumed to be a reduction of the selling prices of the vendor’s products or services and, therefore, are characterized as a reduction of revenue. At the time product is shipped to specialty pharmacies, Kaiser and the specialty distributor to the VA, an adjustment is recorded for estimated rebates, discounts and returns. These allowances are established by management as its best estimate based on available information and will be adjusted to reflect known changes in the factors that impact such allowances. Allowances for rebates, discounts and returns are established based on the contractual terms with customers, historical trends, communications with customers and the levels of inventory remaining in the distribution channel, as well as expectations about the market for the product and anticipated introduction of competitive products.  Product shipping and handling costs are included in cost of sales.  Effective December 1, 2012, the Company no longer accepts returns of Ampyra with the exception of product damages that occur during shipping.

Zanaflex

The Company applies the revenue recognition guidance in Accounting Standards Codification (ASC) 605-15-25, which among other criteria requires that future returns can be reasonably estimated in order to recognize revenue. The amount of future tablet returns is uncertain due to generic competition and customer conversion to Zanaflex Capsules. The Company has accumulated some sales history with Zanaflex Capsules; however, due to existing and potential generic competition and customer conversion from Zanaflex tablets to Zanaflex Capsules, we do not believe we can reasonably determine a return rate at this time. As a result, the Company accounts for these product shipments using a deferred revenue recognition model. Under the deferred revenue model, the Company does not recognize revenue upon product shipment. For these product shipments, the Company invoices the wholesaler, records deferred revenue at gross invoice sales price, and classifies the cost basis of the product held by the wholesaler as a component of inventory. The Company recognizes revenue when prescribed to the end-user, on a first-in first-out (FIFO) basis. The Company’s revenue to be recognized is based on (1) the estimated prescription demand, based on pharmacy sales for its products; and (2) the Company’s analysis of third-party information, including third-party market research data. The Company’s estimates are subject to the inherent limitations of estimates that rely on third-party data, as certain third-party information is itself in the form of estimates, and reflect other limitations. The Company’s sales and revenue recognition reflects the Company’s estimates of actual product prescribed to the end-user. The Company expects to be able to apply a more traditional revenue recognition policy such that revenue is recognized following shipment to the customer when it believes it has sufficient data to develop reasonable estimates of expected returns based upon historical returns and greater certainty regarding generic competition.

The Company’s net revenues represent total revenues less allowances for customer credits, including estimated discounts, rebates, and chargebacks. These allowances are recorded for cash consideration given by a vendor to a customer that is presumed to be a reduction of the selling prices of the vendor’s products or services and, therefore, should be characterized as a reduction of revenue when recognized in the vendor’s statement of operations. Adjustments are recorded for estimated chargebacks, rebates, and discounts. These allowances are established by management as its best estimate based

6

on available information and are adjusted to reflect known changes in the factors that impact such allowances. Allowances for chargebacks, rebates and discounts are established based on the contractual terms with customers, analysis of historical levels of discounts, chargebacks and rebates, communications with customers and the levels of inventory remaining in the distribution channel, as well as expectations about the market for each product and anticipated introduction of competitive products. In addition, the Company records a charge to cost of goods sold for the cost basis of the estimated product returns the Company believes may ultimately be realized at the time of product shipment to wholesalers. The Company has recognized this charge at the date of shipment since it is probable that it will receive a level of returned products; upon the return of such product it will be unable to resell the product considering its expiration dating; and it can reasonably estimate a range of returns. This charge represents the cost basis for the low end of the range of the Company’s estimated returns. Product shipping and handling costs are included in cost of sales.

Milestones and royalties

In order to determine the revenue recognition for contingent milestones, the Company evaluates the contingent milestones using the criteria as provided by the Financial Accounting Standards Boards (FASB) guidance on the milestone method of revenue recognition. At the inception of a collaboration agreement the Company evaluates if payments are substantive.  The criteria requires that (i) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from the Company’s activities to achieve the milestone, (ii) the milestone be related to past performance, and (iii) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement.  If these criteria are met then the contingent milestones can be considered substantive milestones and will be recognized as revenue in the period that the milestone is achieved. Royalties are recognized as earned in accordance with the terms of various research and collaboration agreements.

Collaborations

The Company recognizes collaboration revenues and expenses by analyzing each element of the agreement to determine if it shall be accounted for as a separate element or single unit of accounting. If an element shall be treated separately for revenue recognition purposes, the revenue recognition principles most appropriate for that element are applied to determine when revenue shall be recognized. If an element shall not be treated separately for revenue recognition purposes, the revenue recognition principles most appropriate for the bundled group of elements are applied to determine when revenue shall be recognized. Payments received in excess of revenues recognized are recorded as deferred revenue until such time as the revenue recognition criteria have been met.

Concentration of Risk

Financial instruments that potentially subject the Company to concentrations of credit risk consist principally of investments in cash, cash equivalents, restricted cash and accounts receivable. The Company maintains cash, cash equivalents, restricted cash, short-term and long-term investments with approved financial institutions. The Company is exposed to credit risks and liquidity in the event of default by the financial institutions or issuers of investments in excess of FDIC insured limits. The Company performs periodic evaluations of the relative credit standing of these financial institutions and limits the amount of credit exposure with any institution.

Segment Information

The Company is managed and operated as one business. The entire business is managed by a single management team that reports to the Chief Executive Officer. The Company does not operate separate lines of business with respect to any of its products or product candidates. Accordingly, the Company does not prepare discrete financial information with respect to separate products or product candidates or by location and does not have separately reportable segments.

Subsequent Events

Subsequent events are defined as those events or transactions that occur after the balance sheet date, but before the financial statements are filed with the Securities and Exchange Commission. The Company completed an evaluation of the impact of any subsequent events through the date these financial statements were issued, and determined there were no subsequent events requiring disclosure in or requiring adjustment to these financial statements.

7

Recent Accounting Pronouncements

In February 2013, the FASB amended its guidance to require an entity to present the effect of certain significant reclassifications out of accumulated other comprehensive income on the respective line items in net income. The new accounting guidance does not change the items that must be reported in other comprehensive income or when an item of other comprehensive income must be reclassified to net income. The guidance is effective prospectively for fiscal years beginning after December 15, 2012.  The Company adopted these new provisions for the quarter beginning January 1, 2013. As the guidance requires additional presentation only, there was no impact to the Company’s consolidated results of operations or financial position.

(3) Share-based Compensation

During the three-month periods ended March 31, 2013 and 2012, the Company recognized share-based compensation expense of $4.9 million and $4.2 million, respectively. Activity in options and restricted stock during the three-month period ended March 31, 2013 and related balances outstanding as of that date are reflected below. The weighted average fair value per share of options granted to employees for the three-month periods ended March 31, 2013 and 2012 were approximately $15.41 and $14.15, respectively.

The following table summarizes share-based compensation expense included within the consolidated statements of operations:

	For the three-month
	period ended March 31,
(In thousands)	2013			2012
Research and development		$	1,151		$	989
Selling, general and administrative			3,782			3,202
Total		$	4,933		$	4,191

A summary of share-based compensation activity for the three-month period ended March 31, 2013 is presented below:

Stock Option Activity

	Number of Shares (In thousands)			Weighted Average Exercise Price		Weighted Average Remaining Contractual Term		Intrinsic Value (In thousands)
Balance at January 1, 2013		5,667		$	22.30
Granted		1,315			30.29
Cancelled		(20	)		27.26
Exercised		(89	)		21.50
Balance at March 31, 2013		6,873		$	23.82		7.03	$	57,595
Vested and expected to vest at March 31, 2013		6,778		$	23.76		7.00	$	57,245
Vested and exercisable at March 31, 2013		3,785		$	20.66		5.38	$	43,903

8

Restricted Stock Activity

(In thousands) Restricted Stock	Number of Shares
Nonvested at January 1, 2013	458
Granted	210
Vested	—
Forfeited	(1)
Nonvested at March 31, 2013	667

Unrecognized compensation cost for unvested stock options and restricted stock awards as of March 31, 2013 totaled $56.8 million and is expected to be recognized over a weighted average period of approximately 2.9 years.

 (4) Earnings Per Share

The following table sets forth the computation of basic and diluted earnings per share for the three-month periods ended March 31, 2013 and 2012:

(In thousands, except per share data)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Basic and diluted
Net (loss) income	$	(1,139	)	$	7,846
Weighted average common shares outstanding used in computing net (loss) income per share—basic		39,832			39,340
Plus: net effect of dilutive stock options and restricted common shares		—			1,067
Weighted average common shares outstanding used in computing net (loss) income per share—diluted		39,832			40,407
Net (loss) income per share—basic	$	(0.03	)	$	0.20
Net (loss) income per share—diluted	$	(0.03	)	$	0.19

The difference between basic and diluted shares is that diluted shares include the dilutive effect of the assumed exercise of outstanding securities. The Company’s stock options and unvested shares of restricted common stock could have the most significant impact on diluted shares.

Securities that could potentially be dilutive are excluded from the computation of diluted earnings per share when a loss from continuing operations exists or when the exercise price exceeds the average closing price of the Company’s common stock during the period, because their inclusion would result in an anti-dilutive effect on per share amounts.

The following amounts were not included in the calculation of net (loss) income per diluted share because their effects were anti-dilutive:

(In thousands)	Three-month period ended March 31, 2013	Three-month period ended March 31, 2012
Denominator
Stock options and restricted common shares	7,540	5,189
Convertible note	39	48

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 (5) Income Taxes

For the three-month periods ended March 31, 2013 and 2012, the Company recorded a $1.8 million benefit from and a $372,000 provision for income taxes, respectively, based upon its estimated tax liability for the year. The benefit / provision for income taxes is based on federal, state and Puerto Rico income taxes. The effective income tax rates for the Company for the three-month periods ended March 31, 2013 and 2012 were (60.9)% and 4.5%, respectively. The effective tax rate for the three-month period ended March 31, 2013 benefited from the Company's loss during the three-month period ending March 31, 2013. In addition, as a result of the January 2013 extension of the Federal research and development tax credit retroactive to January 2012 the Company recorded a benefit of $1.2 million for the estimated 2012 credit. During the three-month period ended March 31, 2013 the Company also settled an IRS examination of their corporate income tax returns for years ending December 31, 2009 through December 31, 2011.  The impact of the settlement partially offset the benefit recorded for the research and development tax credit.

The Company continues to evaluate the realizability of its deferred tax assets and liabilities on a periodic basis and will adjust such amounts in light of changing facts and circumstances including, but not limited to, future projections of taxable income, tax legislation, rulings by relevant tax authorities, the progress of ongoing tax audits and the regulatory approval of products currently under development. Any changes to the valuation allowance or deferred tax assets in the future would impact the Company's income taxes.

(6) Fair Value Measurements

The following table presents information about the Company’s assets and liabilities measured at fair value on a recurring basis as of March 31, 2013 and indicates the fair value hierarchy of the valuation techniques utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability. The Company’s Level 1 assets consist of time deposits and investments in a Treasury money market fund and the Company’s Level 2 assets consist of high-quality government bonds and are valued using market prices on the active markets.  Level 1 instrument valuations are obtained from real-time quotes for transactions in active exchange markets involving identical assets and Level 2 assets are valued using quoted prices for similar assets and liabilities in active markets or other market observable inputs such as interest rates and yield curves. The Company’s Level 3 liability represents our put/call liability related to the Paul Royalty Fund (PRF) transaction. No changes in valuation techniques or inputs occurred during the three months ended March 31, 2013.

(In thousands)	Level 1		Level 2		Level 3
March 31, 2013
Assets Carried at Fair Value:
Cash equivalents	$	16,294	$	—	$	—
Short-term investments		—		248,659		—
Long-term investments		—		41,559		—
Liabilities Carried at Fair Value:
Put/call liability		—		—		247
December 31, 2012
Assets Carried at Fair Value:
Cash equivalents	$	27,932	$	—	$	—
Short-term investments		—		191,949		—
Long-term investments		—		99,363		—
Liabilities Carried at Fair Value:
Put/call liability		—		—		329

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The following table presents additional information about assets and/or liabilities measured at fair value on a recurring basis and for which the Company utilizes Level 3 inputs to determine fair value.

(In thousands)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Put/call liability:
Balance, beginning of period	$	329		$	1,030
Total realized and unrealized gains included in selling, general and administrative expenses:		(82	)		(535	)
Balance, end of period	$	247		$	495

The Company estimates the fair value of its put/call liability using a discounted cash flow valuation technique. Using this approach, historical and expected future cash flows are calculated over the expected life of the PRF agreement, are discounted, and then exercise scenario probabilities are applied. Some of the more significant assumptions made in the valuation include (i) the estimated Zanaflex revenue forecast and (ii) the likelihood of put/call exercise trigger events such as bankruptcy and change of control. The valuation is performed periodically when the significant assumptions change.  Realized gains and losses are included in selling, general and administrative expenses.

The put/call liability has been classified as a Level 3 liability as its valuation requires substantial judgment and estimation of factors that are not currently observable in the market due to the lack of trading in the security. If different assumptions were used for the various inputs to the valuation approach including, but not limited to, assumptions involving the estimated Zanaflex revenue forecast and the likelihood of trigger events, the estimated fair value could be significantly higher or lower than the fair value we determined. The Company may be required to record losses in future periods, which may be significant.

(7) Investments

The Company has determined that all of its investments are classified as available-for-sale. Available-for-sale securities are carried at fair value with interest on these securities included in interest income and are recorded based primarily on quoted market prices. Available-for-sale securities consisted of the following:

(In thousands)	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Estimated fair value
March 31, 2013
US Treasury bonds	$	290,081	$	137	$	—		$	290,218
December 31, 2012
US Treasury bonds		291,209		104		(1	)		291,312

The contractual maturities of short-term available-for-sale debt securities at March 31, 2013 and December 31, 2012 are greater than 3 months but less than 1 year. The contractual and intended maturities of long-term available-for-sale debt securities at March 31, 2013 and December 31, 2012 are greater than 1 year and up to 15 months. The Company has determined that there were no other-than-temporary declines in the fair values of its investments as of March 31, 2013.

Short-term investments with maturity of three months or less from date of purchase have been classified as cash equivalents, and amounted to $16.3 million and $27.9 millionas of March 31, 2013 and December 31, 2012, respectively.

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The Company holds available-for-sale investment securities which are reported at fair value on the Company’s balance sheet. Unrealized holding gains and losses are reported within accumulated other comprehensive income (AOCI) in the statements of comprehensive (loss) income.  The changes in AOCI associated with the unrealized holding gain on available-for-sale investments during the three months ended March 31, 2013, were as follows (in thousands):

(In thousands)	Net Unrealized Gains (Losses) on Marketable Securities		Total
Balance at December 31, 2012	$	62	$	62
Other comprehensive income before reclassifications:		21		21
Amounts reclassified from accumulated other        comprehensive income		—		—
Net current period other comprehensive income		21		21
Balance at March 31, 2013	$	83	$	83

(8) Collaborations, Alliances, and Other Agreements

Biogen

On June 30, 2009, the Company entered into an exclusive collaboration and license agreement with Biogen Idec International GmbH (Biogen Idec) to develop and commercialize Ampyra (known as Fampyra outside the U.S.) in markets outside the United States (the “Collaboration Agreement”). Under the Collaboration Agreement, Biogen Idec was granted the exclusive right to commercialize Ampyra and other products containing aminopyridines developed under that agreement in all countries outside of the United States, which grant includes a sublicense of the Company’s rights under an existing license agreement between the Company and Alkermes plc (Alkermes), formerly Elan Corporation, plc (Elan). Biogen Idec has responsibility for regulatory activities and future clinical development of Fampyra in ex-U.S. markets worldwide. The Company also entered into a related supply agreement with Biogen Idec (the “Supply Agreement”), pursuant to which the Company will supply Biogen Idec with its requirements for the licensed products through the Company’s existing supply agreement with Alkermes.

Under the Collaboration Agreement, the Company was entitled to an upfront payment of $110.0 million as of June 30, 2009, which was received in July 2009, and a $25 million milestone payment upon approval of the product in the European Union, which was received in August 2011. The Company is also entitled to receive additional payments of up to $10 million based on the successful achievement of future regulatory milestones and up to $365 million based on the successful achievement of future sales milestones. Due to the uncertainty surrounding the achievement of the future regulatory and sales milestones, these payments will not be recognized as revenue unless and until they are earned. The Company is not able to reasonably predict if and when the milestones will be achieved. Under the Collaboration Agreement, Biogen Idec will be required to make double-digit tiered royalty payments to the Company on ex-U.S. sales. In addition, the consideration that Biogen Idec will pay for licensed products under the Supply Agreement will reflect the price owed to the Company’s suppliers under its supply arrangements with Alkermes or other suppliers for ex-U.S. sales. The Company and Biogen Idec may also carry out future joint development activities regarding licensed product under a cost-sharing arrangement. Under the terms of the Collaboration Agreement, the Company, in part through its participation in joint committees with Biogen Idec, will participate in overseeing the development and commercialization of Ampyra and other licensed products in markets outside the United States pursuant to that agreement. Acorda will continue to develop and commercialize Ampyra independently in the United States.

As of June 30, 2009, the Company recorded a license receivable and deferred revenue of $110.0 million for the upfront payment due to the Company from Biogen Idec under the Collaboration Agreement. Also, as a result of such payment to Acorda, a payment of $7.7 million became payable by Acorda to Alkermes and was recorded as a cost of license payable and deferred expense. The payment of $110.0 million was received from Biogen Idec on July 1, 2009 and the payment of $7.7 million was made to Alkermes on July 7, 2009.

The Company considered the following deliverables with respect to the revenue recognition of the $110.0 million upfront payment:  (1) the license to use the Company’s technology, (2) the Collaboration Agreement to develop and commercialize licensed product in all countries outside the U.S., and (3) the Supply Agreement. Due to the inherent uncertainty in obtaining regulatory approval, the applicability of the Supply Agreement is outside the control of the Company

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and Biogen Idec. Accordingly, the Company has determined the Supply Agreement is a contingent deliverable at the onset of the agreement.  As a result, the Company has determined the Supply Agreement does not meet the definition of a deliverable that needs to be accounted for at the inception of the arrangement. The Company has also determined that there is no significant and incremental discount related to the supply agreement since Biogen Idec will pay the same amount for inventory that the Company would pay and the Company effectively acts as a middle man in the arrangement for which it adds no significant value due to various factors such as the Company does not have any manufacturing capabilities or other knowhow with respect to the manufacturing process.

The Company has determined that the identified non-contingent deliverables (deliverables 1 and 2 immediately preceding) would have no value on a standalone basis if they were sold separately by a vendor and the customer could not resell the delivered items on a standalone basis, nor does the Company have objective and reliable evidence of fair value for the deliverables. Accordingly, the non-contingent deliverables are treated as one unit of accounting.  As a result, the Company will recognize the non-refundable upfront payment from Biogen Idec as revenue and the associated payment to Alkermes as expense ratably over the estimated term of regulatory exclusivity for the licensed products under the Collaboration Agreement as the Company had determined this was the most probable expected benefit period. The Company recognized $2.3 million in license revenue, a portion of the $110.0 million received from Biogen Idec, and $159,000 in cost of license revenue, a portion of the $7.7 million paid to Alkermes, during the three-month periods ended March 31, 2013 and 2012.

On January 21, 2011 Biogen Idec announced that the European Medicines Agency’s (EMA) Committee for Medicinal Products for Human Use (CHMP) decided against approval of Fampyra to improve walking ability in adult patients with multiple sclerosis.  Biogen Idec, working closely with the Company, filed a formal appeal of the decision.  In May 2011, the CHMP recommended conditional marketing authorization, and in July 2011 Biogen Idec received conditional approval from the European Commission for, Fampyra (prolonged-release fampridine tablets) for the improvement of walking in adult patients with MS with walking disability (Expanded Disability Status Scale of 4-7). The Company currently estimates the recognition period to be approximately 12 years from the date of the Collaboration Agreement. As part of its ex-U.S. license agreement, Biogen Idec owes Acorda royalties based on ex-U.S. net sales, and milestones based on ex-U.S. regulatory approval, new indications, and ex-U.S. net sales.  These milestones included a $25 million payment for approval of the product in the European Union which was recorded and paid in the three month period ended March 31, 2012. Based on Acorda’s worldwide license and supply agreement with Alkermes, Alkermes received 7% of this milestone payment from Acorda during the same period.  For revenue recognition purposes, the Company determined this milestone to be substantive in accordance with applicable accounting guidance related to milestone revenue.  Substantive uncertainty existed at the inception of the arrangement as to whether the milestone would be achieved because of the numerous variables, such as the high rate of failure inherent in the research and development of new products and the uncertainty involved with obtaining regulatory approval. Biogen Idec leveraged Acorda’s U.S. Ampyra study results that contributed to the regulatory approval process. Therefore, the milestone was achieved based in part on Acorda’s past performance.  The milestone was also reasonable relative to all deliverable and payment terms of the collaboration arrangement. Therefore, the payment was recognized in its entirety as revenue and the cost of the milestone revenue was recognized in its entirety as an expense during the three-month period ended March 31, 2012.

Actavis/Watson

The Company has an agreement with Watson Pharma, Inc., a subsidiary of Actavis, Inc. (formerly Watson Pharmaceuticals, Inc.), to market tizanidine hydrochloride capsules, an authorized generic version of Zanaflex Capsules, which was launched in February 2012.  In accordance with the Watson agreement, the Company receives a royalty based on Watson’s gross margin, as defined by the agreement, of the authorized generic product. During the three-month periods ended March 31, 2013 and 2012, the Company recognized royalty revenue of $2.6 million and $1.5 million, respectively, related to the gross margin of the Zanaflex Capsule authorized generic.  During the three-month periods ended March 31, 2013 and 2012, the Company also recognized revenue and a corresponding cost of sales of $493,000 and $1.1 million, respectively, related to the purchase and sale of the related Zanaflex Capsule authorized generic product to Watson, which is recorded in net product revenues and cost of sales.

Neuronex

In December 2012, the Company acquired Neuronex, Inc., a privately-held development stage pharmaceutical company (Neuronex).  Neuronex is developing Diazepam Nasal Spray under Section 505(b)(2) of the Food, Drug and Cosmetic Act as an acute treatment for selected, refractory patients with epilepsy, on stable regimens of antiepileptic drugs, or AEDs, who require intermittent use of diazepam to control bouts of increased seizure activity also known as cluster or acute repetitive seizures, or ARS. 

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Under the terms of the agreement, the Company made an upfront payment of $2.0 million in February 2012.  The Company also paid $1.5 million during the twelve month period ended December 31, 2012 pursuant to a commitment under the agreement to fund research to prepare for the Diazepam Nasal Spray pre-NDA meeting with the FDA.  In December 2012, the Company completed the acquisition by paying $6.8 million to former Neuronex shareholders less a $300,000 holdback provision to be settled in December 2013.

The former equity holders of Neuronex are entitled to receive from Acorda up to an additional $18 million in contingent earnout payments upon the achievement of specified regulatory and manufacturing-related milestones with respect to the Diazepam Nasal Spray product, and up to $105 million upon the achievement of specified sales milestones with respect to the Diazepam Nasal Spray product.  The former equity holders of Neuronex will also be entitled to receive tiered royalty-like earnout payments, ranging from the upper single digits to lower double digits, on worldwide net sales of Diazepam Nasal Spray products.  These payments are payable on a country-by-country basis until the earlier to occur of ten years after the first commercial sale of a product in such country and the entry of generic competition in such country as defined in the Agreement.

The patent and other intellectual property and other rights relating to the Diazepam Nasal Spray product are licensed from SK Biopharmaceuticals Co., Ltd. (SK).  Pursuant to the SK license, which granted worldwide rights to Neuronex, except certain specified Asian countries, the Company’s subsidiary Neuronex is obligated to pay SK up to $8 million upon the achievement of specified development milestones with respect to the Diazepam Nasal Spray product and up to $3 million upon the achievement of specified sales milestones with respect to the Diazepam Nasal Spray product.  Also, Neuronex is obligated to pay SK a tiered, mid-single digit royalty on net sales of Diazepam Nasal Spray products.

The Company evaluated the transaction based upon the guidance of ASC 805, Business Combinations, and concluded that it will only acquire inputs and did not acquire any processes.  The Company will need to develop its own processes in order to produce an output. Therefore the Company accounted for the transaction as an asset acquisition and accordingly the $2.0 million upfront payment, $1.5 million in research funding and $6.8 million of closing consideration net of tangible net assets acquired of $3.7, million which were primarily the taxable amount of net operating loss carryforwards, were expensed as research and development expense during the twelve-month period ended December 31, 2012.

(9) Commitments and Contingencies

A summary of the Company’s commitments and contingencies was included in the Company’s Annual Report on Form 10-K for the twelve-month period ended December 31, 2012. The Company’s long-term contractual obligations include commitments and estimated purchase obligations entered into in the normal course of business.   

The Company accrues for amounts related to legal matters if it is probable that a liability has been incurred and the amount is reasonably estimable. While losses, if any, are possible the Company is not able to estimate any ranges of losses as of March 31, 2013. Litigation expenses are expensed as incurred.

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Item 2.  Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis of our consolidated financial condition and results of operations should be read in conjunction with our unaudited consolidated financial statements and related notes included in this Quarterly Report on Form 10-Q.

Background

We are a commercial-stage biopharmaceutical company dedicated to the identification, development and commercialization of novel therapies that improve neurological function in people with multiple sclerosis, or MS, spinal cord injury, or SCI, and other disorders of the nervous system.

Ampyra

General

Ampyra was approved by the FDA in January 2010 for the improvement of walking in people with MS. To our knowledge, Ampyra is the first and only product approved for this indication. Efficacy was shown in people with all four major types of MS (relapsing remitting, secondary progressive, progressive relapsing and primary progressive).  Ampyra was made commercially available in the United States in March 2010.  Net revenue for Ampyra was $62.3 million for the three-months ended March 31, 2013 and $57.4 million for the three-months ended March 31, 2012.

More than 75,000 new patients have tried Ampyra therapy since the 2010 launch.  As of March 2013, approximately 70% of all people with MS who were prescribed Ampyra received a first refill, and approximately 40% of all people with MS who were prescribed Ampyra have been dispensed at least six months of the medicine through refills, consistent with previously reported trends.

Ampyra is marketed in the United States through our own specialty sales force and commercial infrastructure. We currently have approximately 90 sales representatives in the field calling on a priority target list of approximately 7,000 physicians.  We also have established teams of Medical Science Liasons, Regional Reimbursement Directors, and Managed Markets Account Directors who provide information and assistance to payers and physicians on Ampyra, and Market Development Managers who work collaboratively with field teams and corporate personnel to assist in the execution of the Company’s strategic initiatives.

Ampyra is distributed in the United States exclusively through:  a limited network of specialty pharmacy providers that deliver the medication to patients by mail; Kaiser Permanente, which distributes Ampyra to patients through a closed network of on-site pharmacies; and ASD Specialty Healthcare, Inc. (an AmerisourceBergen affiliate), which is the exclusive specialty pharmacy distributor for Ampyra to the U.S. Bureau of Prisons and the U.S. Department of Veterans Affairs, or VA.  All of these customers are contractually obligated to hold no more than an agreed number of days of inventory, ranging from 10 to 30 days.

We have contracted with a third party organization with extensive experience in coordinating patient benefits to run Ampyra Patient Support Services, or APSS, a dedicated resource that coordinates the prescription process among healthcare providers, people with MS, and insurance carriers.  Processing of most incoming requests for prescriptions by APSS begins within 24 hours of receipt. Patients will experience a range of times to receive their first shipment based on the processing time for insurance requirements. As with any prescription product, patients who are members of benefit plans that have restrictive prior authorizations may experience delays in receiving their prescription.

Three of the largest national health plans in the U.S. – Aetna, United Healthcare and Cigna – have listed Ampyra in the lowest branded co-pay tier of their commercial preferred drug list or formulary.  This formulary status at all three health plans was renewed in 2012.  Approximately 75% of commercially insured individuals in the U.S. continue to have no or limited prior authorization requirements, or PA’s, for Ampyra.  We define limited PAs as those that require only an MS diagnosis, documentation of no contraindications, and/or simple documentation that the patient has a walking impairment; such documentation may include a Timed 25-Foot Walk (T25W) test.  The access figure is calculated based on the number of pharmacy lives reported by commercial health plans.

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License and Collaboration Agreement with Biogen Idec

Ampyra is marketed as Fampyra outside the U.S. by Biogen Idec International GmbH, or Biogen Idec, under a license and collaboration agreement that we entered into in June 2009.  Fampyra is commercially available in a number of European Union countries and in Canada, Australia, New Zealand and Israel, and Biogen Idec anticipates making Fampyra commercially available in additional markets in 2013, and anticipates regulatory approval in other countries.  We received a $25 million milestone payment from Biogen Idec in 2011, which was triggered by Biogen Idec’s receipt of conditional approval from the European Commission for Fampyra.  The next expected milestone payment would be $15 million, due when ex-U.S. net sales exceed $100 million over four consecutive quarters.

Ampyra Patent Update

We have three issued patents listed in the Orange Book for Ampyra, as follows:

· The first is U.S. Patent No. US 8,007,826 with claims relating to methods to improve walking in patients with MS by administering 10 mg of sustained release 4-aminopyridine (dalfampridine) twice daily. Based on the final patent term adjustment calculation of the United States Patent and Trademark Office, or USPTO, this patent will extend into 2027.

· The second is U.S. Patent No. 5,540,938 (“the ‘938 patent”), the claims of which relate to methods for treating a neurological disease, such as MS, and cover the use of a sustained release dalfampridine formulation, such as AMPYRA (dalfampridine) Extended Release Tablets, 10 mg for improving walking in people with MS.  In October 2012, the USPTO determined that the ‘938 patent is entitled to a full five year patent term extension under the patent restoration provisions of the Hatch Waxman Act.  With a five year patent term extension, the ‘938 patent would expire in 2018.  We have an exclusive license to this patent from Alkermes (originally with Elan, but transferred to Alkermes as part of its acquisition of Elan’s Drug Technologies business).

· The third, which issued in January  2013, is U.S. Patent No. 8,354,437, which includes claims relating to methods to improve walking, increase walking speed, and treat walking disability in patients with MS by administering 10 mg of sustained release 4-aminopyridine (dalfampridine) twice daily.

In 2011, the European Patent Office, or EPO, granted the counterpart European patent to U.S. Patent No. 8,354,437 with claims relating to, among other things, use of a sustained release aminopyridine composition, such as dalfampridine, to increase walking speed.  In March 2012, Synthon B.V. and neuraxpharm Arzneimittel GmBH filed oppositions with the EPO challenging this granted European patent.  We intend to vigorously defend the European patent, although the outcome of opposition proceedings is unpredictable.

Zanaflex

Zanaflex Capsules and Zanaflex tablets are FDA-approved as short-acting drugs for the management of spasticity, a symptom of many central nervous system, or CNS, disorders, including MS and SCI. These products contain tizanidine hydrochloride, one of the two leading drugs used to treat spasticity.  We launched Zanaflex Capsules in April 2005 as part of our strategy to build a commercial platform for the potential market launch of Ampyra.  Combined net revenue of Zanaflex Capsules and Zanaflex tablets was $1.3 million for the three-months ended March 31, 2013 and $7.2 million for the three-months ended March 31, 2012.  In 2012, Apotex Inc. commercially launched a generic version of tizanidine hydrochloride capsules, and we also launched our own authorized generic version, which is being marketed by Watson Pharma (a subsidiary of Actavis).  In March 2013, Mylan Pharmaceuticals commercially launched their own generic version of Zanaflex Capsules.  The commercial launch of generic tizanidine hydrochloride capsules has caused a significant decline in net revenue of Zanaflex Capsules, and the launch of these generic versions and the potential launch of other generic versions is expected to cause the Company’s net revenue from Zanaflex Capsules to decline further in 2013 and beyond.

Research & Development Programs

We are developing what we believe is one of the industry’s leading pipelines of novel neurological therapies.  We are developing Diazepam Nasal Spray, which we acquired in December 2012, for the treatment of certain epileptic seizures.  We are also studying dalfampridine extended release tablets to improve a range of functional impairments, in addition to walking disability, caused by MS, as well as its potential use in other neurological conditions, including cerebral palsy and

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post-stroke deficits.  In addition, we have several research and development programs focused on distinct therapeutic approaches to restoring neurologic and/or cardiac function.  We are developing the clinical stage compounds AC105 for acute treatment of SCI, GGF2 for the treatment of heart failure, and rHIgM22, a remyelenating monoclonal antibody, for the treatment of MS.  GGF2 is also being investigated in preclinical studies as a treatment for neurological conditions such as stroke and peripheral nerve injury.  Chondroitinase, an enzyme that encourages nerve plasticity in SCI, is in preclinical development.  We believe these programs for restoring neurologic and/or cardiac function have the potential to be first-in-class therapies, and may be applicable across a number of CNS disorders, including stroke and TBI, because many of the mechanisms of tissue damage and repair are similar.

In April 2013, we signed an agreement with NeurogesX, Inc. to purchase from it rights to two assets in the United States, Canada, Latin America and certain other markets excluding Europe.  The first asset is NGX-1998, a phase III ready product that we plan to evaluate for its potential to treat neuropathic pain, beginning with painful diabetic neuropathy.  The second is Qutenza, a patch approved for the treatment of postherpetic neuralgia.  The active ingredient in both NGX-1998 and Qutenza is capsaicin.  The closing of the transaction is still subject to NeurogesX shareholder approval and other customary closing conditions and contingencies.  The terms of the deal are consistent with our business strategy to in-license late-stage and commercial products that leverage our neurology expertise and infrastructure.

Diazepam Nasal Spray

In February 2012, we signed an agreement to acquire Neuronex, Inc., a privately-held pharmaceutical company developing a proprietary nasal spray formulation of diazepam as an acute treatment for selected, refractory patients with epilepsy, on stable regimens of antiepileptic drugs, or AEDs, who require intermittent use of diazepam to control bouts of increased seizure activity, also known as cluster or acute repetitive seizures, or ARS.  We completed the acquisition of Neuronex in December 2012.  Continuing with efforts commenced by Neuronex prior to the acquisition, pending additional clinical and manufacturing data, we plan to submit a 505(b)(2)-type New Drug Application, or NDA, for Diazepam Nasal Spray, to the FDA in 2013, with potential FDA approval and commercial launch in 2014. We anticipate that our current infrastructure can support sales and marketing of this product, and market planning is underway.  A 505(b)(2) application allows for an NDA that references medical literature and the FDA’s finding of safety and effectiveness for a previously approved drug product.  In March 2013 at the American Academy of Neurology annual meeting, we announced data from a Phase 1 study of Diazepam Nasal Spray that showed a single dose of 20 mg Diazepam Nasal Spray had comparable bioavailability to 20 mg of diazepam rectal gel.

Ampyra Development Programs

We believe there may be potential for Ampyra to be applied to other indications within MS and also in other neurological conditions.  For example, we have conducted a Phase 2 proof-of-concept trial of dalfampridine extended release tablets in post-stroke deficits.  This study, which was initiated in 2012, explored the use of dalfampridine in patients who have experienced a stroke at least 6 months prior to enrollment and who have stabilized with chronic neurologic deficits, which may include impaired walking, motor and sensory function and manual dexterity.  Over the first six months following a stroke, patients typically show some degree of spontaneous recovery of function, which may be enhanced by rehabilitation and physical therapy.  This trial targeted motor impairments that remain after such recovery.  In April 2013, we announced that data from the proof-of-concept trial showed improved walking in people with post-stroke deficits.  We plan to proceed with a clinical development program for this indication.  Also,in December 2011, we initiated a Phase 2 proof-of-concept clinical study of dalfampridine in adults with cerebral palsy, or CP.  The first phase of this proof-of-concept study was a single-dose phase primarily to evaluate safety and tolerability prior to proceeding to a multi-dose cohort.  This 10-person, single dose phase of the study detected no safety signals that would prevent additional study of the drug in the treatment of CP.  After completing this first phase, we initiated the second phase a multi-dose study including 24 adults with CP, to evaluate both safety and efficacy.  In April 2013, we announced that efficacy from this study suggested potential treatment activity on measures of walking and hand strength, but that these data are still being analyzed to determine if they are sufficiently robust to warrant further clinical studies.  We plan to present data from both the post-stroke deficits and CP trials in appropriate medical forums following additional analysis of the data.  We also are providing grants for investigator-initiated studies looking for potential benefits on a range of functional deficits in MS and other neurological disorders.  We are also working with external partners on a once-daily formulation of Ampyra.

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AC105

In June 2011, we entered into a License Agreement with Medtronic, Inc. and one of its affiliates, pursuant to which we acquired worldwide development and commercialization rights to certain formulations of magnesium with a polymer such as polyethylene glycol (which we refer to as AC105).  Pursuant to the License Agreement, we paid Medtronic an upfront fee of $3 million and are obligated to pay up to an additional $32 million upon the achievement of specified regulatory and development milestones.  If we commercialize AC105, we will also be obligated to pay a single-digit royalty on sales. We plan to study AC105 as an acute treatment for patients who have suffered neurological trauma, such as SCI and TBI.  We submitted a Phase 2 clinical trial protocol for AC105 for acute treatment of SCI to the FDA for review.  The protocol has been reviewed by the FDA, and we are preparing to initiate the trial in the second half of 2013, pending results of additional preclinical studies.

Glial Growth Factor 2

We have completed a GGF2 Phase 1 clinical trial in heart failure patients.  This was a dose-escalating trial designed to test the maximum tolerated single dose, with follow-up assessments at one, three, and six months.  In March 2013, we presented three-month data from this clinical trial in a platform presentation at the American College of Cardiology (ACC) annual meeting. These data showed a dose-related improvement in ejection fraction in addition to safety findings.  We have discussed the data with the FDA and have reached agreement on the outline of the next clinical study of GGF2 in heart failure, which we plan to initiate by the end of 2013.  This study will primarily investigate further the safety profile of GGF2 across a range of doses, and will continue to explore efficacy outcomes.  If we are able to establish a proof of concept for treatment of heart failure through human clinical studies, we may decide to develop the product independently or to enter into a partnership, most likely with a cardiovascular-focused company.

Remyelinating Antibodies

We have an open IND application for one of the remyelinating antibodies, rHIgM22, for the treatment of MS.  In April 2013, we initiated a Phase 1 clinical trial of rHIgM22 to assess the safety and tolerability of rHIgM22 in patients with MS.  The study also includes several exploratory efficacy measures.

Chondroitinase Program

We are continuing research on the potential use of chondroitinases for the treatment of injuries to the brain and spinal cord, as well as other neurotraumatic indications.  The chondroitinase program is in the research and translational development phase and has not yet entered formal preclinical development.

Outlook for 2013

Financial Guidance for 2013

We are providing the following guidance with respect to our 2013 financial performance:

· We expect 2013 net revenue from the sale of Ampyra to range from $285 million to $315 million.

· We expect Zanaflex (tizanidine hydrochloride) and ex-U.S. Fampyra 2013 revenue to be $25 million, which includes sales of branded Zanaflex products, royalties from ex-U.S. Fampyra and authorized generic tizanidine hydrochloride capsules sales, and $9.1 million in amortized licensing revenue from the $110 million payment we received from Biogen Idec in 2009 for Fampyra ex-U.S. development and commercialization rights.

· Research and development expenses in 2013 are expected to range from $60 million to $70 million, excluding share-based compensation charges.  Research and development expenses in 2013 related to Ampyra include proof-of-concept studies in CP and post-stroke deficits, and sponsorship of investigator-initiated studies. Additional expenses include clinical trials for AC105 and rHIgM22, continued development of Diazepam Nasal Spray and GGF2, as well as ongoing preclinical studies.  A substantial portion of the increase in research and development in 2013 over 2012 is related to Diazepam Nasal Spray expenses. This guidance excludes costs associated with the acquisition of NeurogesX, Inc. assets.

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· Selling, general and administrative expenses in 2013 are expected to range from $170 million to $180 million, excluding share-based compensation charges. SG&A expenses will be primarily driven by commercial and administrative costs related to Ampyra.  The majority of the increase in SG&A in 2013 over 2012 is related to Diazepam Nasal Spray expenses. This guidance excludes costs associated with the acquisition of NeurogesX, Inc. assets.

· We expect to be cash flow positive in 2013. This guidance excludes costs associated with the acquisition of NeurogesX, Inc. assets.

The range of SG&A and R&D expenditures for 2013 are non-GAAP financial measures because they exclude share-based compensation charges and costs associated with the acquisition of NeurogesX, Inc. assets.  Non-GAAP financial measures are not an alternative for financial measures prepared in accordance with GAAP.  However, we believe the presentation of these non-GAAP financial measures, when viewed in conjunction with actual GAAP results, provides investors with a more meaningful understanding of our projected operating performance because they exclude non-cash charges that are substantially dependent on changes in the market price of our common stock and expenses that do not arise from the ordinary course of our business.  We believe these non-GAAP financial measures help indicate underlying trends in our business, and are important in comparing current results with prior period results and understanding expected operating performance.  Also, our management uses these non-GAAP financial measures to establish budgets and operational goals, and to manage our business and to evaluate its performance.

Development Pipeline Goals

Our planned goals and key initiatives with respect to our development pipeline in 2013 are as follows:

·   Pending additional clinical and manufacturing data, submit a 505(b)(2)-type New Drug Application for Diazepam Nasal Spray to the FDA in 2013, with potential FDA approval and commercial launch in 2014.

·   Further analyze  data from our Phase 2 proof-of-concept clinical trial of patients with post-stroke deficits to better understand the entirety of the results, and discuss a planned development program with the FDA.

·   Continue to assess data from our Phase 2 proof-of-concept trial in adults with CP to determine if the data are sufficiently robust to warrant further clinical studies.

·   Continue to progress our Phase 1 clinical trial of rHIgM22, which we initiated in April 2013.

·   Initiate our next clinical study of GGF2 in heart failure by the end of 2013, which will primarily investigate further the safety profile of GGF2 across a range of doses, and will continue to explore efficacy outcomes.

·   Initiate a Phase 2 clinical trial of AC105 for acute treatment of SCI in the second half of 2013, pending results from additional preclinical studies.

·   Continue funding of investigator-initiated studies of Ampyra in MS, focused on a range of functional deficits in MS and other neurological disorders.

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Results of Operations

Three-Month Period Ended March 31, 2013 Compared to March 31, 2012

Net Product Revenues

Ampyra

We recognize product sales of Ampyra following shipment of product to our network of specialty pharmacy providers, Kaiser and the specialty distributor to the VA.  We recognized net revenue from the sale of Ampyra to these customers of $62.3 million as compared to $57.4 million for the three-month periods ended March 31, 2013 and 2012, respectively, an increase of $4.9 million, or 9%.  The net revenue increase was comprised of price increases and discount and allowance adjustments of $4.9 million. Effective January 2, 2013, we increased our sale price to our customers by 10.75%.

Discounts and allowances which are included as an offset in net revenue consists of allowances for customer credits, including estimated chargebacks, rebates, discounts and returns. Discounts and allowances are recorded following shipment of Ampyra tablets to our network of specialty pharmacy providers, Kaiser and the specialty distributor to the VA. Adjustments are recorded for estimated chargebacks, rebates, and discounts.  Discounts and allowances also consist of discounts provided to Medicare beneficiaries whose prescription drug costs cause them to be subject to the Medicare Part D coverage gap (i.e., the “donut hole”).  Payment of coverage gap discounts is required under the Affordable Care Act, the health care reform legislation enacted in 2010.  Discounts and allowances may increase as a percentage of sales as we enter into managed care contracts or amend specialty pharmacy contracts in the future.

The net revenue for the three-month period ended March 31, 2013, decreased from net revenue of $72.4 million for the three-month period ended December 31, 2012.  We believe that the decrease in net revenue between the fourth quarter of 2012 and the first quarter of 2013 reflects certain recurring seasonal factors relating to the commencement of a new calendar year.  These factors include people switching insurance plans or pharmacy benefit providers at year-end.  Consequently, many patients have to re-establish eligibility during the first few months of the calendar year.  Also, when deductibles and the Medicare donut hole reset at the beginning of the calendar year, it can affect timely refills for consumers with financial constraints. In addition, as in previous years, there was some inventory build in the fourth quarter of 2012 that was destocked during the first quarter.

Zanaflex

We recognize product sales of Zanaflex Capsules and Zanaflex tablets using a deferred revenue recognition model where shipments to wholesalers are recorded as deferred revenue and only recognized as revenue when end-user prescriptions of the product are reported. We also recognize product sales on the transfer price of product sold for an authorized generic of Zanaflex Capsules during the three-month period ended March 31, 2013.  We recognized net revenue from the sale of Zanaflex Capsules and Zanaflex tablets of $1.3 million for the three-month period ended March 31, 2013, as compared to $7.2 million for the three-month period ended March 31, 2012. The decrease was due to the commercial launch of generic versions of tizanidine hydrochloride capsules in February 2012.  Net product revenues also include $493,000, which represents the sale of Zanaflex Capsules authorized generic product to Actavis for the three-month period ended March 31, 2012.  Generic competition has caused a significant decline in sales of Zanaflex Capsules and is expected to cause the Company’s net revenue from Zanaflex Capsules to decline further in 2013 and beyond.  In March 2013, Mylan Pharmaceuticals commercially launched their own generic version of Zanaflex Capsules.  The decrease in net revenues was also the result of a disproportionate decrease in discounts and allowances due to the mix of customers continuing to purchase our product. These customers receive higher levels of rebates and allowances.

Discounts and allowances, which are included as an offset in net revenue, consist of allowances for customer credits, including estimated chargebacks, rebates, and discounts.  Adjustments are recorded for estimated chargebacks, rebates, and discounts.

License Revenue

We recognized $2.3 million in license revenue for the three-month periods ended March 31, 2013 and 2012, related to the $110.0 million received from Biogen Idec in 2009 as part of our collaboration agreement. We currently estimate the recognition period to be approximately 12 years from the date of the Collaboration Agreement.

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Royalty Revenues

We recognized $2.9 million and $1.8 million in royalty revenue for the three-month periods ended March 31, 2013 and 2012, respectively related to ex-U.S. sales of Fampyra by Biogen Idec. In 2011, the German government implemented new legislation to manage pricing related to new drug products introduced within the German market through a review of each product’s comparative efficacy. Biogen Idec launched Fampyra in Germany in August 2011. During the three-month period ended June 30, 2012, the government agency completed its comparative efficacy assessment of Fampyra indicating a range of pricing below Biogen Idec’s initial launch price, which was unregulated for the first 12 months after launch consistent with German law. The Company recognized royalty revenue during a portion of 2012 based on the lowest point of the initially indicated German pricing authority range.  Biogen Idec signed the pricing agreement during the three-month period ended March 31, 2013 and the Company recognized additional royalty revenue related to 2012, contributing to the increase in royalty revenue as compared to the three-month period ended March 31, 2013.

We also recognized $2.6 million and $1.5 million in royalty revenue for the three-month periods ended March 31, 2013 and 2012, respectively, related to the authorized generic sale of Zanaflex Capsules which started in February 2012.

Cost of Sales

Ampyra

We recorded cost of sales of $12.7 million for the three-month period ended March 31, 2013 as compared to $10.3 million for the three-month period ended March 31, 2012. Cost of sales for the three-month period ended March 31, 2013 consisted primarily of $10.9 million in inventory costs related to recognized revenues.  The cost of Ampyra inventory is based on a percentage of net product sales of the product in the quarter shipped to Acorda by Alkermes or our alternative manufacturer.  Cost of sales for the three-month period ended March 31, 2013 also consisted of $1.6 million in royalty fees based on net sales, $147,000 in amortization of intangible assets, and $22,000 in period costs related to freight and stability testing.

Cost of sales for the three-month period ended March 31, 2012 consisted primarily of $8.8 million in inventory costs related to recognized revenues.  Cost of sales for the three-month period ended March 31, 2012 also consisted of $1.2 million in royalty fees based on net sales, $147,000 in amortization of intangible assets, and $56,000 in period costs related to freight and stability testing.

Zanaflex

We recorded cost of sales of $331,000 for the three-month period ended March 31, 2013 as compared to $1.2 million for the three-month period ended March 31, 2012. Cost of sales for the three-month period ended March 31, 2013 consisted of $193,000 in inventory costs primarily related to recognized revenues, $98,000 in royalty fees based on net product shipments, and $40,000 in period costs related to packaging, freight and stability testing. Cost of sales also includes $493,000, which represents the cost of Zanaflex Capsules authorized generic product sold for the three-month period ended March 31, 2013.

Cost of sales for the three-month period ended March 31, 2012 included $628,000 in inventory costs related to recognized revenues, $449,000 in royalty fees based on net product shipments, and $12,000 in period costs related to packaging, freight, and stability testing.  Payments to and interest expense related to the PRF transaction discussed below in the section titled “Liquidity and Capital Resources” do not impact the Company’s cost of sales.

Cost of License Revenue

We recorded cost of license revenue of $159,000 and $159,000 for the three-month periods ended March 31, 2013 and 2012, respectively.  Cost of license revenue represents the recognition of a portion of the deferred $7.7 million paid to Alkermes plc (Alkermes), formerly Elan Corporation, plc (Elan) in 2009 in connection with the $110.0 million received from Biogen Idec as a result of our collaboration agreement.

Research and Development

Research and development expenses for the three-month period ended March 31, 2013 were $12.5 million as compared to $11.0 million for the three-month period ended March 31, 2012, an increase of approximately $1.5 million, or 14%. The increase was primarily due to an increase in overall research and development staff, compensation and related

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expenses of $1.7 million to support the various research and development initiatives.  The increase was also due to an increase of $207,000 in our life cycle management program for Ampyra, a $660,000 increase in Phase 1 GGF2 preclinical and clinical trial expenses, a $370,000 increase in technical operations costs associated with our various pipeline initiatives (exclusive of Neuronex expenses), an increase of $340,000 in regulatory costs associated with our various pipeline initiatives, and an increase of $250,000 in preclinical expenses for the remyelinating antibodies program (rHIgM22).  The increases in research and development expenses for the three-month period ended March 31, 2013 were partially offset by a decrease of $1.8 million in Neuronex related expenses attributable to a $2.5 million charge per the terms of the agreement we entered into with Neuronex during the first quarter of 2012, offset by $710,000 in current year research and development expenses related to Diazepam Nasal Spray.  The increases in research and development expenses for the three-month period ended March 31, 2013 were further offset by a decrease of $245,000 related to AC105.

Selling, General and Administrative

Sales and marketing expenses for the three-month period ended March 31, 2013 were $29.5 million compared to $25.1 million for the three-month period ended March 31, 2012, an increase of approximately $4.4 million, or 18%.  The increase was attributable to an increase in overall compensation, benefits, and other selling expenses attributable to Ampyra of $2.3 million. The increase was also related to an increase in overall marketing, selling, distribution, and market research expenses for Ampyra of $1.4 million as well as an increase of $864,000 for pre-launch activities associated with the possible commercialization of  Diazepam Nasal Spray, if approved.  These increases were partially offset by a decrease in sales and marketing expenses for Zanaflex Capsules of $134,000 due to the introduction of generic competition in the marketplace.

General and administrative expenses for the three-month period ended March 31, 2013 were $18.7 million compared to $13.7 million for the three-month period ended March 31, 2012, an increase of approximately $5.0 million, or 37%. This increase was the result of an increase of $2.6 million for staff and compensation expenses and other expenses related to supporting the growth of the organization, an increase in medical affairs expenses including educational programs of $545,000, an increase in business development expenses of $592,000 and an increase of $380,000 in safety and surveillance expenses.  It also included a gain on our put/call liability related to the PRF revenue interest agreement due to the introduction of generic competition in the marketplace for Zanaflex Capsules of $453,000.

Other Expense

Other expense was $418,000 for the three-month period ended March 31, 2013 compared to $637,000 for the three-month period ended March 31, 2012, a decrease of approximately $219,000, or 34%. The decrease was due to a decrease in interest expense of $176,000 principally related to the PRF revenue interest agreement due to a decrease in Zanaflex sales.

Benefit from (Provision for) Income Taxes

For the three-month periods ended March 31, 2013 and 2012, we recorded a $1.8 million benefit from and a $372,000 provision for income taxes, respectively, based upon our estimated tax liability for the year. The benefit / provision for income taxes is based on federal, state and Puerto Rico income taxes. The effective income tax rates for the three-month periods ended March 31, 2013 and 2012 were (60.9)% and 4.5%, respectively. The effective tax rate for the three-month period ended March 31, 2013 benefited from the Company's loss during the three-month period ending March 31, 2013. In addition, as a result of the January 2013 extension of the Federal research and development tax credit retroactive to January 2012 we recorded a benefit of $1.2 million for the estimated 2012 credit.  During the three-month period ended March 31, 2013 the Company also settled an IRS examination of their corporate income tax returns for years ending December 31, 2009 through December 31, 2011.  The impact of the settlement partially offset the benefit recorded for the research and development tax credit.

We continue to evaluate the realizability of its deferred tax assets and liabilities on a periodic basis and will adjust such amounts in light of changing facts and circumstances including, but not limited to, future projections of taxable income, tax legislation, rulings by relevant tax authorities, the progress of ongoing tax audits and the regulatory approval of products currently under development. Any changes to the valuation allowance or deferred tax assets in the future would impact the Company's income taxes.

Liquidity and Capital Resources

Since our inception, we have financed our operations primarily through private placements and public offerings of our common stock and preferred stock, payments received under our collaboration and licensing agreements, sales of

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Ampyra and Zanaflex Capsules, and, to a lesser extent, from loans, government grants and our financing arrangement with PRF.

We were cash flow positive in 2012 and, at March 31, 2013, we had $324.9 million of cash, cash equivalents and short-term and long-term investments, compared to $333.2 million at December 31, 2012.  We expect to be cash flow positive in 2013. Any investments classified as long-term had maturity dates of no later than May 31, 2014. We believe that we have sufficient cash, cash equivalents, short-term and long-term investments on hand, in addition to cash expected to be generated from operations, to fund our 2013 business plan, including our currently anticipated development pipeline activities in 2013.

Our future capital requirements will depend on a number of factors, including the amount of revenue generated from sales of Ampyra and Zanaflex Capsules, the continued progress of our research and development activities, the amount and timing of milestone or other payments payable under collaboration, license and acquisition agreements, the costs involved in preparing, filing, prosecuting, maintaining, defending and enforcing patent claims and other intellectual property rights, and the extent to which we acquire or in-license new products and compounds including the development costs relating to those products or compounds.  To the extent our capital resources are insufficient to meet future operating requirements we will need to raise additional capital, reduce planned expenditures, or incur indebtedness to fund our operations. If we require additional financing in the future, we cannot assure you that it will be available to us on favorable terms, or at all.

Financing Arrangements

In January 1997, Elan International Services, Ltd. (EIS) loaned us an aggregate of $7.5 million pursuant to two convertible promissory notes to partly fund our research and development activities. On December 23, 2005, Elan transferred these promissory notes to funds affiliated with Saints Capital.  As of March 31, 2013, $4.3 million of these promissory notes was outstanding, which amount includes accrued interest. The third of seven annual payments on this note was due and paid on the three year anniversary of Ampyra approval on January 22, 2013 and will continue to be paid annually until paid in full.

On December 23, 2005, we entered into a revenue interest assignment agreement with PRF, a dedicated healthcare investment fund, pursuant to which we assigned to PRF the right to a portion of our net revenues (as defined in the agreement) from Zanaflex Capsules, Zanaflex tablets and any future Zanaflex products including the authorized generic version of Zanaflex Capsules being sold by Watson effective in February 2012. To secure our obligations to PRF, we also granted PRF a security interest in substantially all of our assets related to Zanaflex. Our agreement with PRF covers all Zanaflex net revenues generated from October 1, 2005 through and including December 31, 2015, including the authorized generic version of Zanaflex Capsules revenue, unless the agreement terminates earlier. In November 2006, we entered into an amendment to the revenue interest assignment agreement with PRF. Under the terms of the amendment, PRF paid us $5.0 million in November 2006. An additional $5.0 million was due to us if net revenues during the fiscal year 2006 equaled or exceeded $25.0 million. This milestone was met and the receivable was reflected in our December 31, 2006 financial statements. Under the terms of the amendment, we repaid PRF $5.0 million on December 1, 2009 and an additional $5.0 million on December 1, 2010 since the net revenues milestone was met.

Under the agreement and the amendment, PRF is entitled to the following portion of Zanaflex net revenues:

• with respect to Zanaflex net revenues up to and including $30.0 million for each fiscal year during the term of the agreement, 15% of such net revenues;

• with respect to Zanaflex net revenues in excess of $30.0 million but less than and including $60.0 million for each fiscal year during the term of the agreement, 6% of such net revenues; and

• with respect to Zanaflex net revenues in excess of $60.0 million for each fiscal year during the term of the agreement, 1% of such net revenues.

Notwithstanding the foregoing, once PRF has received and retained payments under the agreement that are at least 2.1 times the aggregate amount PRF has paid us under the agreement, PRF will only be entitled to 1% of Zanaflex net revenues. In connection with the transaction, we recorded a liability as of March 31, 2013, referred to as the revenue interest liability, of approximately $2.1 million. We impute interest expense associated with this liability using the effective interest rate method and record a corresponding accrued interest liability. The effective interest rate is calculated based on the rate that would enable the debt to be repaid in full over the life of the arrangement. The interest rate on this liability may vary during the term of the agreement depending on a number of factors, including the level of Zanaflex sales. We currently

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estimate that the imputed interest rate associated with this liability will be approximately 5.7%. Payments made to PRF as a result of Zanaflex sales levels will reduce the accrued interest liability and the principal amount of the revenue interest liability.

Upon the occurrence of certain events, including if we experience a change of control, undergo certain bankruptcy events, transfer any of our interests in Zanaflex (other than pursuant to a license agreement, development, commercialization, co-promotion, collaboration, partnering or similar agreement), transfer all or substantially all of our assets, or breach certain of the covenants, representations or warranties we make under the agreement, PRF may (i) require us to repurchase the rights we sold them at the “put/call price” in effect on the date such right is exercised or (ii) foreclose on the Zanaflex assets that secure our obligations to PRF. Except in the case of certain bankruptcy events, if PRF exercises its right, which we refer to as PRF’s put option, to cause us to repurchase the rights we assigned to it, PRF may not foreclose unless we fail to pay the put/call price as required. If we experience a change of control we have the right, which we refer to as our call option, to repurchase the rights we sold to PRF at the “put/call price” in effect on the date such right is exercised. The put/call price on a given date is the greater of (i) all payments made by PRF to us as of such date, less all payments received by PRF from us as of such date, and (ii) an amount that would generate an internal rate of return to PRF of 25% on all payments made by PRF to us as of such date, taking into account the amount and timing of all payments received by PRF from us as of such date. We have determined that PRF’s put option and our call option meet the criteria to be considered an embedded derivative and should be accounted for as such. Therefore, we recorded a net liability of $247,000 as of March 31, 2013 related to the put/call option to reflect its current estimated fair value. This liability is revalued on an as needed basis to reflect any changes in the fair value and any gain or loss resulting from the revaluation is recorded in earnings.

During any period during which PRF has the right to receive 15% of Zanaflex net revenues (as defined in the agreement), then 8% of the first $30.0 million in payments from Zanaflex sales we receive from wholesalers will be distributed to PRF on a daily basis. Following the end of each fiscal quarter, if the aggregate amount actually received by PRF during such quarter exceeds the amount of net revenues PRF was entitled to receive, PRF will remit such excess to us. If the amount of net revenues PRF was entitled to receive during such quarter exceeds the aggregate amount actually received by PRF during such quarter, we will remit such excess to PRF.

On August 3, 2012, we received a letter from PRF alleging that we breached specified covenants and representations in the PRF agreement and purporting to exercise the put option.  The letter also includes an allegation that PRF has suffered injuries beyond what is covered by their purported exercise of the put option, although it does not specify or quantify those injuries.  We believe that the allegations are without merit and that the put option has not been validly exercised. Although the letter from PRF does not include a purported calculation of the put option price, if it were validly exercised, we estimate that the incremental cost to the Company in excess of amounts already accrued to PRF at March 31, 2013 would be no more than approximately $2.5 million.

Investment Activities

At March 31, 2013, cash, cash equivalents, short-term and long-term investments were approximately $324.9 million, as compared to $333.2 million at December 31, 2012. Our cash and cash equivalents consist of highly liquid investments with original maturities of three months or less at date of purchase and consist of time deposits and investments in a Treasury money market fund and US Treasury bonds. Also, we maintain cash balances with financial institutions in excess of insured limits. We do not anticipate any losses with respect to such cash balances. As of March 31, 2013, our cash and cash equivalents were $34.7 million, as compared to $41.9 million as of December 31, 2012. Our short-term investments consist of US Treasury bonds with original maturities greater than three months and less than one year. The balance of these investments was $248.7 million as of March 31, 2013, as compared to $191.9 million as of December 31, 2012. Our long-term investments consist of US Treasury bonds with original maturities greater than one year. The balance of these investments was $41.6 million as of March 31, 2013, as compared to $99.4 million as of December 31, 2012.

Net Cash (Used in) / Provided by Operations

Net cash used in operations was $7.7 million for the three-month period ending March 31, 2013 while $3.0 million was provided for the three-month period ended March 31, 2012. Cash used in operations for the three-month period ended March 31, 2013 was primarily due to a decrease in working capital items of $9.5 million attributable to an increase in inventory held by the company and payment of accrued and prepaid items partially offset by a decrease in accounts receivable.  Cash used in operations was also attributable to a decrease in non-current portion of deferred license revenue of $2.3 million, a deferred tax benefit of $1.8 million, and a net loss of $1.1 million principally resulting from an overall increase in operating expenses. Cash used in operations was partially offset by a non-cash share-based compensation expense

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of $4.9 million, amortization of net premiums and discounts on investments of $590,000 and depreciation and amortization of $1.4 million.  

Cash provided by operations for the three-month period ended March 31, 2012 was primarily attributable to net income of $7.8 million principally resulting from license and royalty revenues, a non-cash share-based compensation expense of $4.2 million, amortization of net premiums and discounts on investments of $1.5 million, a decrease in accounts receivable of $1.3 million, and depreciation and amortization of $912,000.  Cash provided by operations was partially offset by a net decrease of $9.7 million due to changes in working capital items primarily due to the payment of 2011 accrued expenses and prepaid items during the three-month period ended March 31, 2012 and a decrease in deferred product revenue of $444,000.  These working capital decreases were partially offset by an increase in other current liabilities of $1.8 million related to the build out of our corporate headquarters in Ardsley, New York, plus an increase in our revenue interest liability related to PRF of $421,000.  The offset to cash provided by operations was also attributable to a decrease in non-current portion of deferred license revenue of $2.3 million due to the amortization of the upfront collaboration payment received during the three-month period ended September 30, 2009, a decrease in the loss on our put/call liability of $535,000, and an increase in inventory held by the Company.

Net Cash Used in Investing

Net cash used in investing activities for the three-month period ended March 31, 2013 was $1.2 million, primarily due to $27.5 million in purchases of investments, purchases of property and equipment of $1.1 million, and purchases of intangible assets of $641,000 , partially offset by $28.0 million in proceeds from maturities and sales of investments.

Net Cash Provided by Financing

Net cash provided by financing activities for the three-month period ended March 31, 2013 was $1.6 million, primarily due to $1.9 million in net proceeds from the issuance of common stock and exercise of stock options partially offset by $265,000 in repayments to PRF.

Contractual Obligations and Commitments

A summary of our minimum contractual obligations related to our major outstanding contractual commitments is included in our Annual Report on Form 10-K for the year ended December 31, 2012. Our long-term contractual obligations include commitments and estimated purchase obligations entered into in the normal course of business. Under certain supply agreements and other agreements with manufacturers and suppliers, we are required to make payments for the manufacture and supply of our clinical and approved products. During the three-month period ended March 31, 2013, commitments related to the purchase of inventory consistent with our normal course of business increased as compared to December 31, 2012. As of March 31, 2013, we have inventory-related purchase commitments totaling approximately $18.8 million.

Under certain license agreements, we are required to pay royalties for the use of technologies and products in our R&D activities and in the commercialization of products. The amount and timing of any of the foregoing payments are not known due to the uncertainty surrounding the successful research, development and commercialization of the products. 

Under certain license agreements, we are also required to pay license fees and milestones for the use of technologies and products in our R&D activities and in the commercialization of products. As of March 31, 2013, we have committed to make potential future milestone payments to third parties of up to approximately $202 million as part of our various collaborations, including licensing and development programs. Payments under these agreements generally become due and payable only upon achievement of certain developmental, regulatory or commercial milestones. Because the achievement of these milestones had not occurred as of March 31, 2013, such contingencies have not been recorded in our financial statements. Amounts related to contingent milestone payments are not considered contractual obligations as they are contingent on the successful achievement of certain development, regulatory approval and commercial milestones. There is uncertainty regarding the various activities and outcomes needed to reach these milestones, and they may not be achieved.

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Critical Accounting Policies and Estimates

Our critical accounting policies are detailed in our Annual Report on Form 10-K for the year ended December 31, 2012. As of March 31, 2013, our critical accounting policies have not changed materially from December 31, 2012.

Item 3.  Quantitative and Qualitative Disclosures About Market Risk

Our financial instruments consist of cash equivalents, short-term and long-term investments, grants receivable, convertible notes payable, accounts payable, and put/call liability. The estimated fair values of all of our financial instruments approximate their carrying amounts at March 31, 2013.

We have cash equivalents, short-term and long-term investments at March 31, 2013, which are exposed to the impact of interest rate changes and our interest income fluctuates as our interest rates change. Due to the nature of our investments in money market funds and US Treasury bonds, the carrying value of our cash equivalents and short-term and long-term investments approximate their fair value at March 31, 2013. Our investments designated as long-term as of March 31, 2013 had maturity dates no later than May 31, 2014.  At March 31, 2013, we held $324.9 million in cash, cash equivalents, short-term and long-term investments which had an average interest rate of approximately 0.05%.

We maintain an investment portfolio in accordance with our investment policy. The primary objectives of our investment policy are to preserve principal, maintain proper liquidity and to meet operating needs. Although our investments are subject to credit risk, our investment policy specifies credit quality standards for our investments and limits the amount of credit exposure from any single issue, issuer or type of investment. Our investments are also subject to interest rate risk and will decrease in value if market interest rates increase. However, due to the conservative nature of our investments and relatively short duration, interest rate risk is mitigated. We do not own derivative financial instruments. Accordingly, we do not believe that there is any material market risk exposure with respect to derivative or other financial instruments.

Item 4.  Controls and Procedures

Evaluation of disclosure controls and procedures

As required by Rule 13a-15 under the Securities Exchange Act of 1934 (the “Exchange Act”) we carried out an evaluation of the effectiveness of our disclosure controls and procedures as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act, as of the end of the first quarter of 2013, the period covered by this report. This evaluation was carried out under the supervision and with the participation of our management, including our chief executive officer and our chief financial officer. Based on that evaluation, these officers have concluded that, as of March 31, 2013, our disclosure controls and procedures were effective to achieve their stated purpose.

Disclosure controls and procedures are controls and other procedures that are designed to ensure that information required to be disclosed in our reports filed or submitted under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules, regulations, and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed in our reports filed or submitted under the Exchange Act is accumulated and communicated to management, including our chief executive officer and chief financial officer, as appropriate, to allow timely decisions regarding disclosure.

Change in internal control over financial reporting

In connection with the evaluation required by Exchange Act Rule 13a-15(d), our management, including our chief executive officer and chief financial officer, concluded that there were no changes in our internal control over financial reporting during the quarter ended March 31, 2013, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

Limitations on the effectiveness of controls

Our disclosure controls and procedures are designed to provide reasonable, not absolute, assurance that the objectives of our disclosure control system are met. Because of inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues, if any, within a company have been detected.

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PART II—OTHER INFORMATION

Item 1.  Legal Proceedings

In August 2007, we received a Paragraph IV Certification Notice from Apotex Inc., advising that it had submitted an Abbreviated New Drug Application, or ANDA, to the FDA seeking marketing approval for generic versions of Zanaflex Capsules.  In response to the filing of the ANDA, in October 2007, we filed a lawsuit against Apotex in the U.S. District Court for the District of New Jersey asserting infringement of our U.S. Patent No. 6,455,557.  In September 2011, the Court ruled against us and, following our appeal, in June 2012 the U.S. Court of Appeals for the Federal Circuit affirmed the decision.  We did not seek any further appeals of the decision.  On September 6, 2011, we filed a citizen petition with the FDA requesting that the FDA not approve Apotex’s ANDA because of public-safety concerns about Apotex’s proposed drug.  On December 2, 2011, Apotex filed suit against us in the U.S. District Court for the Southern District of New York.  In that suit, Apotex alleged, among other claims, that we engaged in anticompetitive behavior and false advertising in connection with the development and marketing of Zanaflex Capsules, including that the citizen petition we filed with the FDA delayed FDA approval of Apotex’s generic tizanidine capsules.  On January 26, 2012, we moved to dismiss or stay Apotex’s suit.  On February 3, 2012, the FDA denied the citizen petition that we filed and approved Apotex’s ANDA for a generic version of Zanaflex Capsules.  On February 21, 2012, Apotex filed an amended complaint that incorporated the FDA action, but otherwise made allegations similar to the original complaint.  Requested judicial remedies include monetary damages, disgorgement of profits, recovery of litigation costs, and injunctive relief.  Following our filing of a motion to dismiss the amended complaint, in 2013 the Court dismissed five of the six counts in the amended complaint, including all of the antitrust claims, leaving only a claim under the Lanham Act relating to alleged product promotional activities.  The case is now proceeding, and the Company intends to defend itself vigorously in the litigation.

Item 1A.  Risk Factors

In addition to the other information set forth in this report, you should carefully consider the risk factors discussed in Part I, “Item 1A. Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2012, all of which could materially affect our business, financial condition or future results. These risks are not the only risks facing our Company. Additional risks and uncertainties not currently known to us or that we currently deem to be immaterial also may materially adversely affect our business, financial condition and/or operating results.

Item 6.  Exhibits

Exhibit No.	Description
10.1	Amendment No. 3 to the Amended and Restated License Agreement and the Supply Agreement, dated February 14, 2013, between the Registrant and Alkermes Pharma Ireland Limited (as successor in interest to Elan Corporation, plc).
10.2*	Addendum Number 3 to Collaboration and License Agreement and to Supply Agreement, dated February 14, 2013, between the Registrant and Biogen Idec International GmbH.
31.1	Certification by the Chief Executive Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934.
31.2	Certification by the Chief Financial Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934.
32.1	Certification by the Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2	Certification by the Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS**	XBRL Instance Document
101.SCH**	XBRL Taxonomy Extension Schema Document
101.CAL**	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF**	XBRL Taxonomy Extension Definition Linkbase Document
101.LAB**	XBRL Taxonomy Extension Label Linkbase Document
101.PRE**	XBRL Taxonomy Extension Presentation Linkbase Document

*Portions of this exhibit were redacted pursuant to a confidential treatment request filed with the Secretary of the Securities and Exchange Commission pursuant to Rule 24b-2 under the Securities Exchange Act of 1934, as amended.

** In accordance with Regulation S-T, the XBRL-related information in Exhibit 101 to this Quarterly Report on Form 10-Q shall be deemed to be “furnished” and not “filed.”

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SIGNATURES

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.

	Acorda Therapeutics, Inc.
	By:	/s/ Ron Cohen
Date:  May 10, 2013		Ron Cohen, M.D. President, Chief Executive Officer and Director (Principal Executive Officer)

	By:	/s/ David Lawrence
Date:  May 10, 2013		David Lawrence, M.B.A. Chief Financial Officer (Principal Financial and Accounting Officer)

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Exhibit Index

Exhibit No.	Description
10.1	Amendment No. 3 to the Amended and Restated License Agreement and the Supply Agreement, dated February 14, 2013, between the Registrant and Alkermes Pharma Ireland Limited (as successor in interest to Elan Corporation, plc).
10.2*	Addendum Number 3 to Collaboration and License Agreement and to Supply Agreement, dated February 14, 2013, between the Registrant and Biogen Idec International GmbH.
31.1	Certification by the Chief Executive Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934.
31.2	Certification by the Chief Financial Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934.
32.1	Certification by the Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2	Certification by the Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101.INS**	XBRL Instance Document
101.SCH**	XBRL Taxonomy Extension Schema Document
101.CAL**	XBRL Taxonomy Extension Calculation Linkbase Document
101.DEF**	XBRL Taxonomy Extension Definition Linkbase Document
101.LAB**	XBRL Taxonomy Extension Label Linkbase Document
101.PRE**	XBRL Taxonomy Extension Presentation Linkbase Document

*Portions of this exhibit were redacted pursuant to a confidential treatment request filed with the Secretary of the Securities and Exchange Commission pursuant to Rule 24b-2 under the Securities Exchange Act of 1934, as amended.

** In accordance with Regulation S-T, the XBRL-related information in Exhibit 101 to this Quarterly Report on Form 10-Q shall be deemed to be “furnished” and not “filed.”

EX-10.1

Exhibit 10.1

CONFIDENTIAL

February 14, 2013

Alkermes Pharma Ireland Limited

Connaught House

1 Burlington Road

Dublin 4, Ireland

Attn:  Kathryn L. Biberstein, Secretary

Re:  Amendment No. 3 to the Amended and Restated License Agreement and the Supply Agreement

Dear Ms. Biberstein:

Acorda Therapeutics, Inc. (“Acorda”) and Alkermes Pharma Ireland Limited (“Alkermes”) have agreed to enter into this Amendment No. 3 to the Amended and Restated License Agreement and the Supply Agreement (“Amendment No. 3”) to establish the basis on which certain payments under the Agreements (as defined below) are made to Alkermes by Acorda pursuant to the Agreements.

Background:

Acorda and Elan Corporation, plc. (“Elan”) were parties to (i) an Amended and Restated License Agreement, dated September 26, 2003, as amended (the “License Agreement”), and (ii) a Supply Agreement, dated September 26, 2003, as amended (the “Supply Agreement” and, collectively, the “Agreements”).  Pursuant to assignments of the Agreements, Alkermes became the successor in interest to all of Elan’s rights and obligations under the Agreements.

Capitalized terms used in this Amendment No. 3 shall have the meaning set forth in the License Agreement or the Supply Agreement (as applicable) unless otherwise defined herein.

Agreement:

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

1.Article 5.6. of the License Agreement.  The title ofArticle 5.6 of the License Agreement shall be deleted in its entirety and replaced with a new title which shall read as follows: “5.6Elan Royalty:”

2.Product Supplied for United States.

a.Article 5.6.1.1 of the License Agreement.  Article 5.6.1.1 of the License Agreement shall be deleted in its entirety and replaced with a new Article 5.6.1.1 which shall read as follows:

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“5.6.1.1 (a) In respect of the Elan Royalty, where Elan manufactures and supplies the Product for use (other than a use covered by other provisions of this Agreement or provisions otherwise agreed to in writing by authorized representatives of the Parties) or sale in the United States, upon delivery of such Product, Elan shall render an invoice to Acorda in respect of the quantities of Product delivered to Acorda for a sum calculated by reference to four per cent (4%) of the then-applicable Notional NSP for the United States and the quantity of such Product supplied. Acorda shall pay this invoice within thirty (30) days of the date of such invoice.

(b) Within forty-five (45) days after the end of each calendar quarter during the term of this Agreement in which any such Product has been supplied pursuant to Article 5.6.1.1(a), Acorda shall, pursuant to Article 5.9.1, provide a Statement to Elan setting forth the actual NSP for Product sold in the United States in such calendar quarter that is relevant to such Product supplied.  The Statement shall also set forth a calculation of the total Elan Royalty payable to Elan for the Product supplied by Elan during such calendar quarter pursuant to Article 5.6.1.1(a) by reference to ten per cent (10%) of such actual NSP and the amount of such Product supplied by Elan.  Acorda will owe Elan the difference between (i) the amount calculated by reference to ten per cent (10%) of such actual NSP and the amount of such Product supplied by Elan, minus (ii) the amount paid or payable pursuant to Article 5.6.1.1(a) for such calendar quarter.  If such difference is positive, Acorda shall pay such amount to Elan within forty-five (45) days after the end of such calendar quarter; if such difference is negative, Elan shall credit such overpayment to Acorda against monies owed for Product subsequently supplied to Acorda pursuant to this Agreement.

(c) For the avoidance of doubt the Parties agree that if for whatever reason the Product supplied by Elan to Acorda pursuant to Article 5.6.1.1(a) during the previous calendar quarter which meets the Specifications and the applicable law and regulatory requirements is not sold by Acorda, payment to Elan of the total Elan Royalty for such Product shall nonetheless be effectedand the price of the Product shall be determined by reference to the NSP calculated pursuant to the provisions of Article 5.6.1.1(b).

For example:  If on January 1, 2012, Elan delivers 1000 units of Product for sale in the United States, upon delivery of such Product, Elan shall render an invoice to Acorda for four per cent (4%) of the then-applicable Notional NSP for the United States of $570.45 for a total amount of $22,818 (4% x $570.45 x 1000).  Acorda shall pay this invoice on or before January 31, 2012.  On or before May 15, 2012, Acorda shall provide a Statement to Elan setting forth the actual NSP of $610 for Product sold in the United States during the calendar quarter ending March 31, 2012.  During the calendar quarter ending March 31, 2012 only 600 units of Product were sold; the

2

remaining 300 units of Product were sold during the calendar quarter ending June 30, 2012 and the final 100 units of Product were never sold.  Notwithstanding the foregoing, on or before May 15, 2012, Acorda shall pay to Elan $38,182 with respect to the 1000 units of Product delivered on January 1, 2012 (10% x $610 x 1000 = $61,000 - $22,818).”

b.Article 9.3.3(a) of the Supply Agreement.  Article 9.3.3 of the Supply Agreement shall be deleted in its entirety and replaced with new Articles 9.3.3(a), 9.3.3(b) and 9.3.3(c).  Article 9.3.3(a) shall read as follows:

“9.3.3 (a) Upon supply to Acorda of Product for use (other than a use covered by other provisions of this Agreement or provisions otherwise agreed to in writing by authorized representatives of the Parties) or sale in the United States, Elan shall render an invoice in respect of the quantities of Product delivered to Acorda for a sum calculated by reference to eight per cent (8%) of the then-applicable Notional NSP for the United States.  Acorda shall pay such invoice within thirty (30) days of the date of such invoice (or, through March 2012, within sixty (60) days of the date of such invoice).  Within forty-five (45) days after the end of each calendar quarter during the term of this Agreement in which Elan has supplied Product pursuant to this Article 9.3.3(a), Acorda shall provide a Statement to Elan setting forth the actual NSP (as defined in the License Agreement) for Product sold in the United States in such calendar quarter that is relevant to such Product supplied, and Acorda will owe Elan the difference between (i) the amount calculated by reference to eight per cent (8%) of such actual NSP and the amount of such Product supplied by Elan in such calendar quarter, which shall be the “Supply Price,” minus (ii) the amount paid or payable pursuant to the previous sentence.  If such difference is positive, Acorda shall pay such amount concurrently with the delivery of such Statement; if such difference is negative, Elan shall credit such overpayment to Acorda against monies owed for Product subsequently supplied to Acorda pursuant to this Agreement.

For example:  If on January 1, 2012, Elan delivers 1000 units of Product for sale in the United States, upon delivery of such Product, Elan shall render an invoice to Acorda for eight per cent (8%) of the then-applicable Notional NSP for the United States of $570.45 for a total amount of $45,636 (8% x $570.45 x 1000).  Acorda shall pay this invoice on or before January 31, 2012.  On or before May 15, 2012, Acorda shall provide a Statement to Elan setting forth the actual NSP of $610 for Product sold in the United States during the calendar quarter ending March 31, 2012.  Concurrently with the delivery of the

Statement, Acorda shall pay to Elan $3,164 with respect to the 1000 units of Product delivered on January 1, 2012 (8% x $610 x 1000 = $48,800 - $45,636).”

c.           Article 5.6.1.3 of the License Agreement.  Article 5.6.1.3 of the License Agreement shall be deleted in its entirety and replaced with a new Article 5.6.1.3 which shall read as follows:

3

“5.6.1.3 In respect of the Elan Royalty, where Elan does not manufacture and supply the Product but the Product is supplied to Acorda by a third party(ies) for use (other than a use covered by other provisions of this Agreement or provisions otherwise agreed to in writing by authorized representatives of the Parties) or sale in the United States, within forty-five (45) days after the end of each calendar quarter during the term of this Agreement in which any such Product has been supplied (or, through March 2012, within sixty (60) days after the end of each such calendar quarter), pursuant to Article 5.9.1, Acorda shall provide a Statement to Elan setting forth the actual NSP for Product sold in the United States in such calendar quarter that is relevant to such Product supplied and the amount of such Product supplied by such third party(ies) in such calendar quarter.  The Statement shall also set forth a calculation of the total Elan Royalty payable to Elan for such Product supplied by such third party(ies) in such calendar quarter by reference to ten per cent (10%) of such actual NSP and the amount of such Product supplied.  Such total Elan Royalty shall be paid by Acorda to Elan within forty-five (45) days after the end of each calendar quarter during the term of this Agreement (or, through March 2012, within sixty (60) days after the end of each calendar quarter during the term of this Agreement).”

3.Product Supplied for Countries other than the United States.

a.Article 5.6.1.2.  Article 5.6.1.2 of the License Agreement shall be deleted in its entirety and replaced with a new Article 5.6.1.2 which shall read as follows:

“5.6.1.2 In respect of the Elan Royalty, where Elan manufactures and supplies the Product for sale in countries other than the United States, within forty-five (45) days after the end of each calendar quarter during the term of this Agreement in which any such Product has been sold, pursuant to Article 5.9.1, Acorda shall provide a Statement to Elan setting forth the actual NSP for Product sold in each such country in such calendar quarter that is relevant to the Product supplied by Elan, on a country-by-country basis.  The Statement shall also set forth a calculation of the total Elan Royalty payable to Elan for such Product supplied by Elan that has been actually sold during such calendar quarter by reference to ten per cent (10%) of such actual NSP and the amount of such Product sold, on a country by country basis.  Such total Elan Royalty shall be paid by or on behalf of Acorda to Elan within forty-five (45) days after the end of each calendar quarter during the term of this Agreement.

For example:  On January 1, 2012, Elan delivers 1000 units of Product for sale in Germany.  During the calendar quarter ending March 31, 2012 only 600 units of Product were sold; during the calendar quarter ending June 30, 2012, 300 units of Product were sold; the remaining 100 units of Product were never sold.  On or before

4

May 15, 2012, Acorda shall provide a Statement to Elan setting forth the actual NSP of $610 for Product sold in Germany during the calendar quarter ending March 31, 2012.  On or before May 15, 2012, Acorda shall pay to Elan $36,600 with respect to the 600 units of Product sold during the calendar quarter ending March 31, 2012 (10% x $610 x 600).  On or before August 14, 2012, Acorda shall provide a Statement to Elan setting forth the actual NSP of $610 for Product sold in Germany during the calendar quarter ending June 30, 2012.  On or before August 14, 2012, Acorda shall pay to Elan $18,300 with respect to the 300 units of Product sold during the calendar quarter ending June 30, 2012 (10% x $610 x300).  Elan shall receive no Elan Royalty for the 100 units of Product that were never sold.”

b.Article 9.3.3(b) of the Supply Agreement.  Article 9.3.3 of the Supply Agreement shall be deleted in its entirety and replaced with new Articles 9.3.3(a), 9.3.3(b) and 9.3.3(c).  Article 9.3.3(b) shall read as follows:

“9.3.3 (b) Upon supply to Acorda of Product for use (other than a use covered by other provisions of this Agreement or provisions otherwise agreed to in writing by authorized representatives of the Parties) or sale in countries other than the United States, Elan shall render an invoice in respect of the quantities of Product delivered to Acorda for a sum calculated by reference to eight per cent (8%) of the then-applicable Notional NSP for each of the countries other than the United States for which such Product was supplied.  Acorda shall pay such invoice within thirty (30) days of the date of such invoice (or, through July 2013, within sixty (60) days of the date of such invoice).  Within forty-five (45) days after the end of each calendar quarter during the term of this Agreement in which Elan has supplied Product pursuant to this Article 9.3.3(b), Acorda shall provide a Statement to Elan setting forth the actual NSP for Product sold in each of the countries other than the United States in such calendar quarter that is relevant to such Product supplied, on a country by country basis, and Acorda will owe Elan the difference between (i) the amount calculated by reference to eight per cent (8%) of such actual NSP and the amount of such Product supplied by Elan in such calendar quarter, on a country by country basis, which shall be the “Supply Price,” minus (ii) the amount paid or payable pursuant to the previous sentence.  If such difference is positive, Acorda shall pay such amount concurrently with the delivery of such Statement; if such difference is negative, Elan shall credit such overpayment to Acorda against monies owed for Product subsequently supplied to Acorda pursuant to this Agreement.

For example:  If on January 1, 2012, Elan delivers 1000 units of Product for sale in Germany, upon delivery of such Product, Elan shall render an invoice to Acorda for eight per cent (8%) of the then-applicable Notional NSP for countries other than the United States of $570.45 for a total amount of $45,636 (8% x $570.45 x 1000).  Acorda shall pay this invoice on or before March 1, 2012.  On or before May 15, 2012, Acorda shall provide a Statement to Elan setting forth the actual NSP of $610 for Product sold in

5

Germany during the calendar quarter ending March 31, 2012.  Concurrently with the delivery of the Statement, Acorda shall pay to Elan $3,164 with respect to the 1000 units of Product delivered on January 1, 2012 (8% x $610 x 1000 = $48,800 - $45,636).”

c.           Article 5.6.1.4 of the License Agreement.  A new Article 5.6.1.4 shall be added to the License Agreement which shall read as follows:

“5.6.1.4 In respect of the Elan Royalty, where Elan does not manufacture and supply the Product but the Product is supplied to Acorda or its Designee by a third party(ies) for sale in countries other than the United States, within forty-five (45) days after the end of each calendar quarter during the term of this Agreement in which any such Product has been sold (or, through July 2013, within sixty (60) days after the end of each such calendar quarter), pursuant to Article 5.9.1, Acorda shall provide a Statement to Elan setting forth the actual NSP for Product sold in each of the countries other than the United States in such calendar quarter that is relevant to the Product supplied by such third party(ies), on a country by country basis.  The Statement shall also set forth a calculation of the total Elan Royalty payable to Elan for such Product supplied by such third party(ies) that has been actually sold during such calendar quarter by reference to ten per cent (10%) of such actual NSP and the amount of such Product sold, on a country by country basis.  Such total Elan Royalty shall be paid by or on behalf of Acorda to Elan within forty-five (45) days after the end of each calendar quarter during the term of this Agreement (or, through July 2013, within sixty (60) days after the end of each calendar quarter during the term of this Agreement).”

4.Article 5.6.1.5 of the License Agreement.  A new Article 5.6.1.5 shall be added to the License Agreement which shall read as follows:

“5.6.1.5 The Parties agree that all examples in this Article 5.6.1 are for illustrative purposes only and are not intended to describe all the possible scenarios with respect to payments under Article 5.6.1 nor are they intended to modify the terms of this Agreement nor is the use of a particular dollar amount for NSP in multiple countries or multiple calendar quarters intended to imply that NSP would not vary between countries and/or between calendar quarters, and Article 5.6.1 shall not be deemed to supersede any provisions of this Agreement that provide for a lower Elan Royalty.”

5.Article 9.3.3(c) of the Supply Agreement.  Article 9.3.3 of the Supply Agreement shall be deleted in its entirety and replaced with new Articles 9.3.3(a), 9.3.3(b) and 9.3.3(c).  Article 9.3.3(c) shall read as follows:

“9.3.3 (c) The Parties agree that all examples in this Article 9.3.3 are for illustrative purposes only and are not intended to describe all the possible

6

scenarios with respect to payments under Article 9.3.3 nor are they intended to modify the terms of this Agreement nor is the use of a particular dollar amount for NSP in multiple countries or multiple calendar quarters intended to imply that NSP would not vary between countries and/or between calendar quarters, and Article 9.3.3 shall not be deemed to supersede any provisions of this Agreement that provide for a lower Supply Price.”

6.Determination of Notional NSP and NSP.  Notional NSP and NSP will be determined based on the sales of Product by Acorda or its Designee to a third party that is not an Affiliate of Acorda or affiliated with its Designee; sales between Acorda and its Designee will also be disregarded.

7.Previous Payments.  The provisions of Sections 1 through 6 and Section 8 of this Amendment No. 3 shall apply to Product manufactured and supplied prior to, on or after the date of this Amendment No. 3, and, notwithstanding Article 5.8 of the License Agreement, any amounts paid to Alkermes pursuant to the Agreements prior to the date of this Amendment No. 3 with respect to any Product manufactured and supplied shall be credited to the amounts due under the Agreements, as modified by this Amendment No. 3.

8.Article 9.6 of the Supply Agreement.  The first two paragraphs of Article 9.6 of the Supply Agreement shall be deleted in their entirety.

9.Notional NSP.  Effective December 31, 2012, the Notional NSP definition in the License Agreement is hereby deleted in its entirety and replaced with a new definition which shall read as follows:

“‘Notional NSP’ shall mean the estimated NSP of Product at the applicable time, which shall be provided by Acorda to Elan for both (i) the United States and (ii) all countries other than the United States, in each case, within ninety (90) days prior to commencement of each calendar year during the term of this Agreement.

Unless otherwise agreed in writing by the Parties, the applicable Notional NSPs shall be calculated by reference to (i) the average NSP in the United States and (ii) the weighted average NSP (by sales volume) in all countries other than the United States, in each case as evidenced by the last four (4) Statements delivered to Elan pursuant to Article 5.9.1.”

10.Notices.  The addresses for notices to Acorda and Alkermes pursuant to Article 12.12.1 of the License Agreement and Article 14.12.1 of the Supply Agreement shall be as follows:

If to Accorda:

Acorda Therapeutics, Inc.

420 Saw Mill River Road

7

Ardsley, New York 10502

United States of America

Attention: Chief Executive Officer

Fax: +1-914-606-9572

With a copy to

Attention: General Counsel

at the same address

Fax: +1-914-606-9737

If to Alkermes:

Alkermes Pharma Ireland Limited

Connaught House

1 Burlington Road

Dublin 4, Ireland

Fax: +353 1 772 8001

Attention: Secretary

With a copy to:

Attention:  Vice President, Alliance Management

at the same address

Fax: +353 1 772 8001

11.No Other Amendments.  Except as expressly set out in this Amendment No. 3, all terms and conditions of the Agreements remain unchanged and continue to be in full force and effect.

12.Counterparts and Facsimile Signatures.  This Amendment No. 3 may be executed in any number of counterparts, each of which shall be deemed an original, and all of which together shall constitute one and the same instrument.  Signatures provided by facsimile transmission or in Adobe™ Portable Document Format (PDF) sent by electronic mail shall be deemed to be original signatures.

13.Modification.  This Amendment No. 3 may not be modified unless such modification is made in writing, references this Amendment No. 3 and is signed by the Parties by their respective officers thereunto duly authorized.

14.Governing Law.  This Amendment No. 3 shall be governed by and construed in accordance with the laws of the State of New York, without regard to its conflicts of laws principles.

15.Severability.  If, under applicable law, any provision of this Amendment No. 3 is determined to be invalid or unenforceable, or otherwise directly or indirectly affects the validity of any other material provision(s) of this Amendment No. 3 (“Severed Clause”), the Parties

8

mutually agree that this Amendment No. 3 shall endure except for the Severed Clause.  The Parties shall consult and use commercially reasonable efforts to agree upon a valid and enforceable provision that shall be a reasonable substitute for such Severed Clause in light of the intent of this Amendment No. 3.

[Remainder of Page Intentionally Left Blank]

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By its signature below, Acorda acknowledges its agreement with the provisions of this Amendment No. 3.  Please sign below to acknowledge Alkermes’ agreement with the provisions of this Amendment No. 3 and return a copy to my attention.

Sincerely,

Acorda Therapeutics, Inc.

By: /s/ Ron Cohen, M.D.

       Ron Cohen, M.D.

       President & CEO

Acknowledged and Agreed on behalf of Alkermes Pharma Ireland Limited:

By: /s/Peter Thornton

Name:  Peter Thornton

Title:  Director

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EX-10.2

EXHIBIT 10.2

CONFIDENTIAL

Addendum Number 3 to Collaboration and License Agreement and to Supply Agreement

This Addendum Number 3 to Collaboration and License Agreement and to Supply Agreement (“Addendum Number 3”) is entered into February 14, 2013 (“Addendum Number 3 Effective Date”), by and between Acorda Therapeutics, Inc. (“Acorda”) and Biogen Idec International GmbH (“Licensee”).  Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the License Agreement (as defined below).

Recitals

WHEREAS, Acorda and Licensee have entered into that certain Collaboration and License Agreement effective as of June 30, 2009, as amended (the “License Agreement”), and the Supply Agreement effective as of June 30, 2009, as amended (the “Supply Agreement”);

WHEREAS, the Parties now wish to amend certain terms and conditions of the License Agreement in accordance with Section 16.12 of the License Agreement and certain terms and conditions of the Supply Agreement in accordance with Section 12.3 of the Supply Agreement;

WHEREAS, Licensee has consented to Amendment No. 3 to the Amended and Restated License Agreement and Supply Agreement between Acorda and Acorda’s license, Alkermes Pharma Ireland Limited (the “Agreements”), which Agreements are Third Party Agreements, as defined in the License Agreement

NOW, THEREFORE, in consideration of the foregoing recitals and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, and intending to be legally bound, the Parties agree as follows:

AGREEMENT:

1.Elan Royalty Rate.  Section 8.3(b) of the License Agreement is hereby deleted in its entirety and replaced with the following new provision with respect to sales beginning in the second Calendar Quarter of 2012:

“(b)           Elan Royalty Rate.  Subject to this Section 8.3, during the Royalty Term, Licensee shall pay to Acorda a royalty of [***] percent ([***]%) of aggregate Net Sales of Licensed Product in the Territory (the “Elan Royalty Rate”), calculated on a country-by-country basis and due in accordance with Section 8.5, which Acorda shall pay to Elan in accordance with the Elan License Agreement; provided, that (A) Licensee shall be responsible for providing in good faith any estimations or subjective determinations that comprise part of the calculation of Notional NSP (as defined in the Elan License Agreement), for the quantities of Licensed Product ordered by or on behalf of Licensee and delivered pursuant to the Supply Agreement, including any orders for Launch Stock, (B) Acorda shall submit to Elan such estimations and subjective determinations provided by Licensee for the purposes of Notional NSP calculation, and (C) Licensee shall be responsible for any payments stemming from such Notional NSP calculation, including any additional payments (including interest payments), in the event that Elan disagrees with Licensee’s calculation and Licensee is unable to reach agreement with Elan regarding the appropriate amount, to the extent required by the Elan License Agreement.  Notwithstanding anything in this Agreement, the amount of the Elan Royalty Rate payable by Licensee to Acorda shall in no event be more than the Elan Royalty (as defined in the Elan License Agreement)

.

Certain portions of this Exhibit have been omitted pursuant to a request for confidentiality. Such omitted portions, which are marked with brackets [ ] and an asterisk*, have been separately filed with the Commission.

CONFIDENTIAL

payable by Acorda to Elan under the Elan License Agreement.  By way of example, if the Elan Royalty Rate is reduced from [***]% to [***]% with respect to a country under the terms of the Elan License Agreement, the Elan Royalty Rate hereunder shall be [***]% with respect to such country.  The Parties acknowledge that the cost of Launch Stocks pursuant to the Supply Agreement is [***] percent ([***]%) of Manufacturing Cost (as defined in the Elan Supply Agreement) and all other Licensed Product supplied to Licensee under the Supply Agreement will be supplied at the applicable Transfer Price (as defined in the Supply Agreement).  The Parties acknowledge that Licensee shall pay Acorda the royalties under the Elan Royalty Rate for sales of Launch Stocks no less than five (5) Business Days before such time as the Elan Royalty Rate with respect thereto is owed to Elan.  Acorda shall provide to Licensee a copy of all royalty reports submitted to Elan pursuant to the Elan Agreement related to payments made pursuant to this Agreement promptly after such reports are submitted to Elan.”

2.Reports and Payments.  The second (2nd) sentence of Section 8.5 of the License Agreement is hereby deleted in its entirety and replaced with the following new provision:  “Such reports shall indicate gross sales and all deductions taken from gross sales and the quantity of Licensed Products sold, on a country-by-country basis, the calculation of Net Sales and the calculation of royalties from Net Sales with respect thereto, each determined in accordance with GAAP.”

3.Transfer Price.  Section 6.2 of the Supply Agreement is hereby deleted in its entirety and replaced with the following new provision:

“6.2           Price and Reimbursements.  The price for Product shall be the Transfer Price.  Upon shipment of the Product, Acorda shall issue an invoice for such shipment.  Such invoice shall list separately those expenses subject to reimbursement by Licensee under this Agreement.  For clarity, with respect to Product supplied to Licensee pursuant to the Elan Supply Agreement, upon supply of such Product, Acorda shall render an invoice in respect of the quantities of Product delivered to Licensee for a sum calculated by reference to [***] per cent ([***]%) of the then-applicable Notional NSP (as defined in the Elan License Agreement) for the countries for which such Product was supplied. Following the end of each Calendar Quarter, Licensee will owe the difference between (i) the amount calculated by reference to [***] per cent ([***]%) of the actual NSP (as defined in the Elan License Agreement) and the amount of the Product supplied by Elan in such Calendar Quarter, on a country-by-country basis (if such information is reasonably available; if not, the Parties shall meet promptly to discuss), minus (ii) the amount paid by Licensee pursuant to the previous sentence with respect to the relevant country.  If such difference is positive, Licensee shall pay such amount in accordance with Section 6.3(c).  If such difference is negative, credits will be handled in accordance with Section 6.3(c).”

4.Remittance of Payments.  The first two sentences of Section 6.4 of the Supply Agreement are hereby deleted in their entirety and replaced with the following new sentences, :

“Through July 2013, all payments from Licensee to Acorda hereunder shall be due within forty-five (45) days after Licensee’s receipt of an invoice therefor or as otherwise set forth in Section 6.3(c) (if earlier).  Thereafter, payment shall be made within twenty (20) days after Licensee’s receipt of an invoice therefor or as otherwise set forth in Section 6.3(c) (if earlier).”

Certain portions of this Exhibit have been omitted pursuant to a request for confidentiality. Such omitted portions, which are marked with brackets [ ] and an asterisk*, have been separately filed with the Commission.

CONFIDENTIAL

5.Credit. On or before the Addendum Number 3 Effective Date, Licensee and Acorda have agreed to and established an outstanding credit amount, a portion of which may be offset against the Elan Royalty Rate owed to Acorda by Licensee each Calendar Quarter.  The credit was established to reflect Licensee’s payment of the [***] percent ([***]%) prepaid portion of the Elan Royalty Rate (in accordance with the provisions of Section 8.3(b) of the License Agreement as in existence prior to the amendment in Section 1 of this Addendum Number 3) on Licensed Product shipped by Elan through the first Calendar Quarter of 2012 and implements the retroactive nature of the deletion of the [***] percent ([***]%) prepayment described in Section 1 of this Addendum Number 3.  Each Calendar Quarter the credit is applied based on the amount of Licensed Product sold by Licensee during such Calendar Quarter, on a unit-by-unit and country-by country basis.  Licensee and Acorda have agreed to continue with such practice until the established credit amount is exhausted.  Thereafter, with respect to any Licensed Product purchased by Licensee from Acorda or directly from Elan or the Second Source prior to the Addendum Number 3 Effective Date, which is not resold by Licensee to a Third Party before such Licensed Product is deemed obsolete and for which Licensee paid Acorda the Elan Royalty Rate (as such term was defined prior to the Addendum Number 3 Effective Date), if Licensee provides written notice to Acorda of such unsold obsolete Licensed Product and the amounts paid to Acorda as the Elan Royalty Rate with respect thereto, then Acorda shall notify Elan thereof and, to the extent, if any, that Elan credits to Acorda any such amounts paid by Licensee to Acorda, Acorda shall credit such amounts to Licensee.

6.Elan Assignment.  The Parties agree and acknowledge that Alkermes Pharma Ireland Limited is the successor in interest to all of Elan Pharma International Limited’s rights and obligations under the Elan License Agreement and the Elan Supply Agreement.

7.Advice of Counsel.  Each Party declares and represents that such Party has carefully read this Addendum Number 3, understands its content, has had the benefit of legal advice with respect to the execution of this Addendum Number 3, and has executed this Addendum Number 3 freely and voluntarily.

8.General.  Except as modified by this Addendum Number 3, the License Agreement and the Supply Agreement are hereby reaffirmed in its entirety by the Parties hereto and shall continue in full force and effect.  This Addendum Number 3 may be executed in any number of counterparts, each of which shall be deemed an original, and all of which together shall constitute one and the same instrument.  Signatures provided by facsimile transmission or in Adobe™ Portable Document Format (PDF) sent by electronic mail shall be deemed to be original signatures.

[Signature page follows.]

Certain portions of this Exhibit have been omitted pursuant to a request for confidentiality. Such omitted portions, which are marked with brackets [ ] and an asterisk*, have been separately filed with the Commission.

CONFIDENTIAL

IN WITNESS WHEREOF, the Parties hereto have caused this Addendum Number 3 to be executed by their respective officers hereunto duly authorized as of the Addendum Number 3 Effective Date.

ACORDA THERAPEUTICS, INC.	BIOGEN IDEC INTERNATIONAL GMBH
By: /s/Ron Cohen, M.D.        Ron Cohen, M.D.        President & CEO	By: /s/Suzanne Delvaque Name:  Suzanne Delvaque Title:  Sr. Director Switzerland Legal

EX-31.1

Exhibit 31.1

CERTIFICATION BY THE CHIEF EXECUTIVE OFFICER PURSUANT TO

RULE 13a-14(a) UNDER THE SECURITIES EXCHANGE ACT OF 1934

I, Ron Cohen, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Acorda Therapeutics, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 10, 2013

/s/ Ron Cohen

Ron Cohen

Chief Executive Officer

(Principal Executive Officer)

EX-31.2

Exhibit 31.2

CERTIFICATION BY THE CHIEF FINANCIAL OFFICER PURSUANT TO

RULE 13a-14(a) UNDER THE SECURITIES EXCHANGE ACT OF 1934

I, David Lawrence, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Acorda Therapeutics, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 10, 2013

/s/ David Lawrence

David Lawrence

Chief Financial Officer

(Principal Financial Officer)

EX-32.1

EXHIBIT 32.1

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO SECTION 906

OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Quarterly Report on Form 10-Q of Acorda Therapeutics, Inc. (the “Company”) for the fiscal quarter ended March 31, 2013, as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Ron Cohen, Chief Executive Officer 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, that:

(1) The Report fully complies with the requirements of Section 13(a) or 15(d), as applicable, of the Securities Exchange Act of 1934, as amended; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

/s/ RON COHEN

RON COHEN

Chief Executive Officer

(Principal Executive Officer)

May 10, 2013

[A signed original of this written statement required by Section 906 of the Sarbanes-Oxley Act of 2002 has been provided to Acorda Therapeutics, Inc. and will be retained by Acorda Therapeutics, Inc. and furnished to the Securities and Exchange Commission or its staff upon request.]

EX-32.2`

EXHIBIT 32.2

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 on Form 10-Q of Acorda Therapeutics, Inc. (the “Company”) for the fiscal quarter ended March 31, 2013, as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, David Lawrence, Chief Financial Officer 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, that:

(1) The Report fully complies with the requirements of Section 13(a) or 15(d), as applicable, of the Securities Exchange Act of 1934, as amended; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

/s/ DAVID LAWRENCE

DAVID LAWRENCE

Chief Financial Officer

(Principal Financial Officer)

May 10, 2013

[A signed original of this written statement required by Section 906 of the Sarbanes-Oxley Act of 2002 has been provided to Acorda Therapeutics, Inc. and will be retained by Acorda Therapeutics, Inc. and furnished to the Securities and Exchange Commission or its staff upon request.]

XML

Earnings Per Share (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Basic and diluted
Net (loss) income	$ (1,139)	$ 7,846
Weighted average common shares outstanding used in computing net (loss) income per share-basic	39,832	39,340
Plus: net effect of dilutive stock options and restricted common shares		1,067
Weighted average common shares outstanding used in computing net (loss) income per share-diluted	39,832	40,407
Net (loss) income per share-basic (in dollars per share)	$ (0.03)	$ 0.20
Net (loss) income per share-diluted (in dollars per share)	$ (0.03)	$ 0.19

XML

Share-based Compensation

3 Months Ended

Mar. 31, 2013

Share-based Compensation

Share-based Compensation

(3) Share-based Compensation

During the three-month periods ended March 31, 2013 and 2012, the Company recognized share-based compensation expense of $4.9 million and $4.2 million, respectively. Activity in options and restricted stock during the three-month period ended March 31, 2013 and related balances outstanding as of that date are reflected below. The weighted average fair value per share of options granted to employees for the three-month periods ended March 31, 2013 and 2012 were approximately $15.41 and $14.15, respectively.

The following table summarizes share-based compensation expense included within the consolidated statements of operations:

	For the three-month
	period ended March 31,
(In thousands)	2013		2012
Research and development	$	1,151	$	989
Selling, general and administrative	3,782		3,202
Total	$	4,933	$	4,191

A summary of share-based compensation activity for the three-month period ended March 31, 2013 is presented below:

Stock Option Activity

	Number of Shares (In thousands)		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Intrinsic Value (In thousands)
Balance at January 1, 2013	5,667		$	22.30
Granted	1,315		30.29
Cancelled	(20	)	27.26
Exercised	(89	)	21.50
Balance at March 31, 2013	6,873		$	23.82	7.03	$	57,595
Vested and expected to vest at March 31, 2013	6,778		$	23.76	7.00	$	57,245
Vested and exercisable at March 31, 2013	3,785		$	20.66	5.38	$	43,903

Restricted Stock Activity

(In thousands) Restricted Stock	Number of Shares
Nonvested at January 1, 2013	458
Granted	210
Vested	—
Forfeited	(1	)
Nonvested at March 31, 2013	667

Unrecognized compensation cost for unvested stock options and restricted stock awards as of March 31, 2013 totaled $56.8 million and is expected to be recognized over a weighted average period of approximately 2.9 years.

XML

Fair Value Measurements (Details 2) (Put/call liability, USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Put/call liability
Put/call liability
Balance, beginning of period	$ 329	$ 1,030
Total realized and unrealized gains included in selling, general and administrative expenses:	(82)	(535)
Balance, end of period	$ 247	$ 495

XML

Fair Value Measurements (Details) (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Assets Carried at Fair Value:
Short-term investments	$ 248,659	$ 191,949
Long-term investments	41,559	99,363
Recurring basis | Level 1
Assets Carried at Fair Value:
Cash equivalents	16,294	27,932
Recurring basis | Level 2
Assets Carried at Fair Value:
Short-term investments	248,659	191,949
Long-term investments	41,559	99,363
Recurring basis | Level 3
Liabilities Carried at Fair Value:
Put/call liability	$ 247	$ 329

XML

Investments (Details) (USD $)	3 Months Ended
	Mar. 31, 2013	Dec. 31, 2012
Investments
Short-term investments classified as cash and cash equivalents	$ 16,300,000	$ 27,900,000
Other-than-temporary declines in the fair values of investments	0
Minimum
Investments
Short-term investments maturity term	3 months
Long-term investments maturity term	1 year
Maximum
Investments
Short-term investments maturity term	1 year
Long-term investments maturity term	15 months
US Treasury bonds
Investments
Amortized Cost	290,081,000	291,209,000
Gross unrealized gains	137,000	104,000
Gross unrealized losses		(1,000)
Estimated fair value	$ 290,218,000	$ 291,312,000

XML

Investments (Details 2) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Changes in accumulated other comprehensive income
Balance at the beginning of the period	$ 62
Other comprehensive income before reclassifications	21
Other comprehensive income (loss), net of tax	21	(100)
Balance at the end of the period	83
Net Unrealized Gain (Loss) on Marketable Securities
Changes in accumulated other comprehensive income
Balance at the beginning of the period	62
Other comprehensive income before reclassifications	21
Other comprehensive income (loss), net of tax	21
Balance at the end of the period	$ 83

XML

Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2013

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

(2) Summary of Significant Accounting Policies

Principles of Consolidation

The accompanying consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States of America and include the results of operations of the Company and its majority owned subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

The preparation of the consolidated financial statements requires management of the Company to make a number of estimates and assumptions relating to the reported amount of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the period. Significant items subject to such estimates and assumptions include share-based compensation accounting, which are largely dependent on the fair value of the Company’s equity securities. In addition, the Company recognizes Zanaflex revenue based on estimated prescriptions filled. The Company adjusts its Zanaflex inventory value based on an estimate of inventory that may be returned. Actual results could differ from those estimates.

Investments

Both short-term and long-term investments consist of US Treasury bonds. The Company classifies marketable securities available to fund current operations as short-term investments in current assets on its consolidated balance sheets. Marketable securities are classified as long-term investments in long-term assets on the consolidated balance sheets if the Company has the ability and intent to hold them and such holding period is longer than one year. The Company classifies its short-term and long-term investments as available-for-sale. Available-for-sale securities are recorded at fair value of the investments based on quoted market prices.

Unrealized holding gains and losses on available-for-sale securities, which are determined to be temporary, are excluded from earnings and are reported as a separate component of accumulated other comprehensive income (loss).

Premiums and discounts on investments are amortized over the life of the related available-for-sale security as an adjustment to yield using the effective-interest method. Dividend and interest income are recognized when earned. Amortized premiums and discounts, dividend and interest income and realized gains and losses are included in interest income.

Accumulated Other Comprehensive Income

The Company’s accumulated other comprehensive income is comprised of gains and losses on available for sale securities and is recorded and presented net of income tax.

Revenue Recognition

Ampyra

                Ampyra is available only through a network of specialty pharmacy providers that provide the medication to patients by mail; Kaiser Permanente (Kaiser), which distributes Ampyra to patients through a closed network of on-site pharmacies; and ASD Specialty Healthcare, Inc. (an AmerisourceBergen affiliate), which is the exclusive specialty pharmacy distributor for Ampyra to the U.S. Bureau of Prisons and the U.S. Department of Veterans Affairs (VA). Ampyra is not available in retail pharmacies. The Company does not recognize revenue from product sales until there is persuasive evidence of an arrangement, delivery has occurred, the price is fixed and determinable, the buyer is obligated to pay the Company, the obligation to pay is not contingent on resale of the product, the buyer has economic substance apart from the Company, the Company has no obligation to bring about the sale of the product, and the amount of returns can be reasonably estimated and collectability is reasonably assured. The Company recognizes product sales of Ampyra following shipment of product to a network of specialty pharmacy providers, Kaiser, and the specialty distributor to the VA. The specialty pharmacy providers, Kaiser, and the specialty distributor to the VA are contractually obligated to hold no more than an agreed number of days of inventory, ranging from 10 to 30 days.

                The Company’s net revenues represent total revenues less allowances for customer credits, including estimated rebates, discounts and returns. These allowances are recorded for cash consideration given by a vendor to a customer that is presumed to be a reduction of the selling prices of the vendor’s products or services and, therefore, are characterized as a reduction of revenue. At the time product is shipped to specialty pharmacies, Kaiser and the specialty distributor to the VA, an adjustment is recorded for estimated rebates, discounts and returns. These allowances are established by management as its best estimate based on available information and will be adjusted to reflect known changes in the factors that impact such allowances. Allowances for rebates, discounts and returns are established based on the contractual terms with customers, historical trends, communications with customers and the levels of inventory remaining in the distribution channel, as well as expectations about the market for the product and anticipated introduction of competitive products.  Product shipping and handling costs are included in cost of sales.  Effective December 1, 2012, the Company no longer accepts returns of Ampyra with the exception of product damages that occur during shipping.

Zanaflex

The Company applies the revenue recognition guidance in Accounting Standards Codification (ASC) 605-15-25, which among other criteria requires that future returns can be reasonably estimated in order to recognize revenue. The amount of future tablet returns is uncertain due to generic competition and customer conversion to Zanaflex Capsules. The Company has accumulated some sales history with Zanaflex Capsules; however, due to existing and potential generic competition and customer conversion from Zanaflex tablets to Zanaflex Capsules, we do not believe we can reasonably determine a return rate at this time. As a result, the Company accounts for these product shipments using a deferred revenue recognition model. Under the deferred revenue model, the Company does not recognize revenue upon product shipment. For these product shipments, the Company invoices the wholesaler, records deferred revenue at gross invoice sales price, and classifies the cost basis of the product held by the wholesaler as a component of inventory. The Company recognizes revenue when prescribed to the end-user, on a first-in first-out (FIFO) basis. The Company’s revenue to be recognized is based on (1) the estimated prescription demand, based on pharmacy sales for its products; and (2) the Company’s analysis of third-party information, including third-party market research data. The Company’s estimates are subject to the inherent limitations of estimates that rely on third-party data, as certain third-party information is itself in the form of estimates, and reflect other limitations. The Company’s sales and revenue recognition reflects the Company’s estimates of actual product prescribed to the end-user. The Company expects to be able to apply a more traditional revenue recognition policy such that revenue is recognized following shipment to the customer when it believes it has sufficient data to develop reasonable estimates of expected returns based upon historical returns and greater certainty regarding generic competition.

The Company’s net revenues represent total revenues less allowances for customer credits, including estimated discounts, rebates, and chargebacks. These allowances are recorded for cash consideration given by a vendor to a customer that is presumed to be a reduction of the selling prices of the vendor’s products or services and, therefore, should be characterized as a reduction of revenue when recognized in the vendor’s statement of operations. Adjustments are recorded for estimated chargebacks, rebates, and discounts. These allowances are established by management as its best estimate based on available information and are adjusted to reflect known changes in the factors that impact such allowances. Allowances for chargebacks, rebates and discounts are established based on the contractual terms with customers, analysis of historical levels of discounts, chargebacks and rebates, communications with customers and the levels of inventory remaining in the distribution channel, as well as expectations about the market for each product and anticipated introduction of competitive products. In addition, the Company records a charge to cost of goods sold for the cost basis of the estimated product returns the Company believes may ultimately be realized at the time of product shipment to wholesalers. The Company has recognized this charge at the date of shipment since it is probable that it will receive a level of returned products; upon the return of such product it will be unable to resell the product considering its expiration dating; and it can reasonably estimate a range of returns. This charge represents the cost basis for the low end of the range of the Company’s estimated returns. Product shipping and handling costs are included in cost of sales.

Milestones and royalties

In order to determine the revenue recognition for contingent milestones, the Company evaluates the contingent milestones using the criteria as provided by the Financial Accounting Standards Boards (FASB) guidance on the milestone method of revenue recognition. At the inception of a collaboration agreement the Company evaluates if payments are substantive.  The criteria requires that (i) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from the Company’s activities to achieve the milestone, (ii) the milestone be related to past performance, and (iii) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement.  If these criteria are met then the contingent milestones can be considered substantive milestones and will be recognized as revenue in the period that the milestone is achieved. Royalties are recognized as earned in accordance with the terms of various research and collaboration agreements.

Collaborations

The Company recognizes collaboration revenues and expenses by analyzing each element of the agreement to determine if it shall be accounted for as a separate element or single unit of accounting. If an element shall be treated separately for revenue recognition purposes, the revenue recognition principles most appropriate for that element are applied to determine when revenue shall be recognized. If an element shall not be treated separately for revenue recognition purposes, the revenue recognition principles most appropriate for the bundled group of elements are applied to determine when revenue shall be recognized. Payments received in excess of revenues recognized are recorded as deferred revenue until such time as the revenue recognition criteria have been met.

Concentration of Risk

Financial instruments that potentially subject the Company to concentrations of credit risk consist principally of investments in cash, cash equivalents, restricted cash and accounts receivable. The Company maintains cash, cash equivalents, restricted cash, short-term and long-term investments with approved financial institutions. The Company is exposed to credit risks and liquidity in the event of default by the financial institutions or issuers of investments in excess of FDIC insured limits. The Company performs periodic evaluations of the relative credit standing of these financial institutions and limits the amount of credit exposure with any institution.

Segment Information

                The Company is managed and operated as one business. The entire business is managed by a single management team that reports to the Chief Executive Officer. The Company does not operate separate lines of business with respect to any of its products or product candidates. Accordingly, the Company does not prepare discrete financial information with respect to separate products or product candidates or by location and does not have separately reportable segments.

Subsequent Events

                Subsequent events are defined as those events or transactions that occur after the balance sheet date, but before the financial statements are filed with the Securities and Exchange Commission. The Company completed an evaluation of the impact of any subsequent events through the date these financial statements were issued, and determined there were no subsequent events requiring disclosure in or requiring adjustment to these financial statements.

Recent Accounting Pronouncements

In February 2013, the FASB amended its guidance to require an entity to present the effect of certain significant reclassifications out of accumulated other comprehensive income on the respective line items in net income. The new accounting guidance does not change the items that must be reported in other comprehensive income or when an item of other comprehensive income must be reclassified to net income. The guidance is effective prospectively for fiscal years beginning after December 15, 2012.  The Company adopted these new provisions for the quarter beginning January 1, 2013. As the guidance requires additional presentation only, there was no impact to the Company’s consolidated results of operations or financial position.

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Collaborations, Alliances, and Other Agreements (Details) (USD $)	3 Months Ended		0 Months Ended	3 Months Ended					3 Months Ended			1 Months Ended	3 Months Ended	12 Months Ended	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Jun. 30, 2009 Biogen Idec	Mar. 31, 2013 Biogen Idec	Mar. 31, 2012 Biogen Idec	Jul. 07, 2009 Biogen Idec	Jul. 01, 2009 Biogen Idec	Jun. 30, 2009 Biogen Idec Maximum	Mar. 31, 2013 Actavis/Watson	Mar. 31, 2012 Actavis/Watson	Dec. 31, 2012 Neuronex	Feb. 29, 2012 Neuronex DZNS	Mar. 31, 2013 Neuronex DZNS	Dec. 31, 2012 Neuronex DZNS	Mar. 31, 2013 Neuronex DZNS Maximum	Mar. 31, 2013 Neuronex DZNS SK Maximum
Collaboration agreement
Deferred license revenue			$ 110,000,000
Cash received							110,000,000
Milestone payment due upon approval of the product in the European Union					25,000,000
Additional payments based on the successful achievement of future regulatory milestones								10,000,000
Contingent receivable based on the successful achievement of future sales milestones								365,000,000
Payment made to third party for cost of license						7,700,000
Amount of significant and incremental discount related to the supply agreement				0
Identified non-contingent deliverables value on standalone basis, if sold separately				0
License Revenue				2,300,000	2,300,000
Cost of license revenue				159,000	159,000
Current estimate of license revenue recognition period			12 years
Portion of milestone payment from Acorda to Alkermes (as a percent)					7.00%
Royalty revenues	5,516,000	3,310,000							2,600,000	1,500,000
Revenue recognized	64,084,000	65,673,000							493,000	1,100,000
Cost of sales	13,484,000	12,464,000							493,000	1,100,000
Business Acquisition
Upfront payments recorded as research and development expense												2,000,000
Advance research funding payments recorded as research and development expense														1,500,000
Payments to complete the acquisition											6,800,000
Tangible net assets acquired, primarily the taxable amount of net operating loss carryforwards											3,700,000
Additional payments upon successful achievement of future regulatory and manufacturing-related milestones															18,000,000
Additional payments upon successful achievement of future sales milestones															105,000,000
Royalty payment period													10 years
Payments Neuronex is obligated to make to SK upon achievement of specified development milestones																8,000,000
Entitlement of additional payments based on the successful achievement of future sales milestones																3,000,000
Holdback provision											$ 300,000

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Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 34,687	$ 41,876
Restricted cash	34	380
Short-term investments	248,659	191,949
Trade accounts receivable, net of allowances of $587 and $555, as of March 31, 2013 and December 31, 2012, respectively	23,288	26,327
Prepaid expenses	7,606	6,936
Finished goods inventory held by the Company	27,850	20,176
Finished goods inventory held by others	736	781
Deferred tax asset	36,955	35,091
Other current assets	11,060	9,547
Total current assets	390,875	333,063
Long-term investments	41,559	99,363
Property and equipment, net of accumulated depreciation	16,936	16,706
Deferred tax asset	101,545	101,636
Intangible assets, net of accumulated amortization	9,446	9,319
Non-current portion of deferred cost of license revenue	4,649	4,808
Other assets	413	437
Total assets	565,423	565,332
Current liabilities:
Accounts payable	24,077	22,503
Accrued expenses and other current liabilities	31,786	35,758
Deferred product revenue-Zanaflex	29,620	29,275
Current portion of deferred license revenue	9,057	9,057
Current portion of revenue interest liability	1,180	1,134
Current portion of convertible notes payable	1,144	1,144
Total current liabilities	96,864	98,871
Non-current portion of deferred license revenue	66,421	68,685
Put/call liability	247	329
Non-current portion of revenue interest liability	891	1,111
Non-current portion of convertible notes payable	3,133	4,244
Other non-current liabilities	6,228	6,171
Commitments and contingencies
Stockholders' equity:
Common stock, $0.001 par value. Authorized 80,000,000 shares at March 31, 2013 and December 31, 2012; issued and outstanding 39,893,408 and 39,804,493 shares, including those held in treasury, as of March 31, 2013 and December 31, 2012, respectively	40	40
Treasury stock at cost (12,420 shares at March 31, 2013 and December 31, 2012)	(329)	(329)
Additional paid-in capital	647,507	640,671
Accumulated deficit	(255,662)	(254,523)
Accumulated other comprehensive income	83	62
Total stockholders' equity	391,639	385,921
Total liabilities and stockholders' equity	$ 565,423	$ 565,332

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Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Cash flows from operating activities:
Net (loss) income	$ (1,139)	$ 7,846
Adjustments to reconcile net income to net cash provided by operating activities:
Share-based compensation expense	4,933	4,191
Amortization of net premiums and discounts on investments	586	1,507
Amortization of revenue interest issuance cost	16	30
Depreciation and amortization expense	1,400	912
Gain on put/call liability	(82)	(535)
Deferred tax benefit	(1,772)
Changes in assets and liabilities:
Decrease in accounts receivable	3,039	1,302
Increase in prepaid expenses and other current assets	(2,183)	(5,459)
Increase in inventory held by the Company	(7,674)	(357)
Decrease in inventory held by others	45	81
Decrease in non-current portion of deferred cost of license revenue	159	159
Decrease (increase) in other assets	8	(92)
Decrease in accounts payable, accrued expenses, other current liabilities	(3,510)	(6,144)
Increase in revenue interest liability interest payable	92	421
Decrease in non-current portion of deferred license revenue	(2,264)	(2,264)
Increase in other non-current liabilities		1,858
Increase (decrease) in deferred product revenue-Zanaflex	345	(444)
Decrease in restricted cash	346
Net cash (used in) provided by operating activities	(7,655)	3,012
Cash flows from investing activities:
Purchases of property and equipment	(1,060)	(3,104)
Purchases of intangible assets	(641)	(656)
Purchases of investments	(27,471)	(65,396)
Proceeds from maturities of investments	28,000	61,750
Net cash used in investing activities	(1,172)	(7,406)
Cash flows from financing activities:
Proceeds from issuance of common stock and option exercises	1,903	1,949
Repayments of revenue interest liability	(265)	(209)
Net cash provided by financing activities	1,638	1,740
Net decrease in cash and cash equivalents	(7,189)	(2,654)
Cash and cash equivalents at beginning of period	41,876	57,954
Cash and cash equivalents at end of period	34,687	55,300
Supplemental disclosure:
Cash paid for interest	466	304
Cash paid for taxes	$ 731	$ 165

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Summary of Significant Accounting Policies (Details 2)	3 Months Ended
	Mar. 31, 2013 item
Segment Information
Number of businesses in operation	1

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Share-based Compensation (Details 2) (USD $) Share data in Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013
Share based compensation, other disclosures
Total unrecognized compensation costs related to unvested options and restricted stock awards that the company expects to recognize	$ 56,800,000
Weighted average period	2 years 10 months 24 days
Stock Options
Stock Option Activity
Beginning balance (in shares)	5,667
Granted (in shares)	1,315
Cancelled (in shares)	(20)
Exercised (in shares)	(89)
Ending balance (in shares)	6,873
Vested and expected to vest at end of period (in shares)	6,778
Vested and exercisable at end of period (in shares)	3,785
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share)	$ 22.30
Granted (in dollars per share)	$ 30.29
Cancelled (in dollars per share)	$ 27.26
Exercised (in dollars per share)	$ 21.50
Balance at the end of the period (in dollars per share)	$ 23.82
Vested and expected to vest at the end of the period (in dollars per share)	$ 23.76
Vested and exercisable at the end of the period (in dollars per share)	$ 20.66
Weighted Average Remaining Contractual Term
Balance at the end of the period	7 years 11 days
Vested and expected to vest at the end of the period	7 years
Vested and exercisable at the end of the period	5 years 4 months 17 days
Intrinsic Value
Balance at the end of the period	57,595,000
Vested and expected to vest at the end of the period	57,245,000
Vested and exercisable at the end of the period	$ 43,903,000
Restricted Stock
Restricted Stock Activity
Nonvested at the beginning of the period (in shares)	458
Granted (in shares)	210
Forfeited (in shares)	(1)
Nonvested at the end of the period (in shares)	667

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Organization and Business Activities

3 Months Ended

Mar. 31, 2013

Organization and Business Activities

Organization and Business Activities

(1) Organization and Business Activities

Acorda Therapeutics, Inc. (“Acorda” or the “Company”) is a commercial stage biopharmaceutical company dedicated to the identification, development and commercialization of novel therapies that improve neurological function in people with multiple sclerosis (MS), spinal cord injury (SCI) and other disorders of the central nervous system.

The management of the Company is responsible for the accompanying unaudited interim consolidated financial statements and the related information included in the notes to the consolidated financial statements. In the opinion of management, the unaudited interim consolidated financial statements reflect all adjustments, including normal recurring adjustments necessary for the fair presentation of the Company’s financial position and results of operations and cash flows for the periods presented. Results of operations for interim periods are not necessarily indicative of the results to be expected for the entire year.

These unaudited interim consolidated financial statements should be read in conjunction with the audited consolidated financial statements of the Company as of and for the year ended December 31, 2012 included in the Company’s Annual Report on Form 10-K for such year, as filed with the Securities and Exchange Commission (the “SEC”).

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Consolidated Balance Sheets (Parenthetical) (USD $) In Thousands, except Share data, unless otherwise specified	Mar. 31, 2013	Dec. 31, 2012
Consolidated Balance Sheets
Trade accounts receivable, allowances (in dollars)	$ 587	$ 555
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, Authorized shares	80,000,000	80,000,000
Common stock, issued shares	39,893,408	39,804,493
Common stock, outstanding shares	39,893,408	39,804,493
Treasury stock, shares	12,420	12,420

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Share-based Compensation (Tables)

3 Months Ended

Mar. 31, 2013

Share-based Compensation

Summary of share-based compensation expense

	For the three-month
	period ended March 31,
(In thousands)	2013		2012
Research and development	$	1,151	$	989
Selling, general and administrative	3,782		3,202
Total	$	4,933	$	4,191

Summary of stock option activity

	Number of Shares (In thousands)		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Intrinsic Value (In thousands)
Balance at January 1, 2013	5,667		$	22.30
Granted	1,315		30.29
Cancelled	(20	)	27.26
Exercised	(89	)	21.50
Balance at March 31, 2013	6,873		$	23.82	7.03	$	57,595
Vested and expected to vest at March 31, 2013	6,778		$	23.76	7.00	$	57,245
Vested and exercisable at March 31, 2013	3,785		$	20.66	5.38	$	43,903

Summary of restricted stock activity

(In thousands) Restricted Stock	Number of Shares
Nonvested at January 1, 2013	458
Granted	210
Vested	—
Forfeited	(1	)
Nonvested at March 31, 2013	667

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Document and Entity Information	3 Months Ended
	Mar. 31, 2013	Apr. 30, 2013
Document and Entity Information
Entity Registrant Name	ACORDA THERAPEUTICS INC
Entity Central Index Key	0001008848
Document Type	10-Q
Document Period End Date	Mar. 31, 2013
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		40,566,088
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q1

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Earnings Per Share (Tables)

3 Months Ended

Mar. 31, 2013

Earnings Per Share

Schedule of computation of basic and diluted earnings per share

(In thousands, except per share data)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Basic and diluted
Net (loss) income	$	(1,139	)	$	7,846
Weighted average common shares outstanding used in computing net (loss) income per share—basic	39,832			39,340
Plus: net effect of dilutive stock options and restricted common shares	—			1,067
Weighted average common shares outstanding used in computing net (loss) income per share—diluted	39,832			40,407
Net (loss) income per share—basic	$	(0.03	)	$	0.20
Net (loss) income per share—diluted	$	(0.03	)	$	0.19

Schedule of antidilutive securities excluded from computation of earnings per share

(In thousands)	Three-month period ended March 31, 2013	Three-month period ended March 31, 2012
Denominator
Stock options and restricted common shares	7,540	5,189
Convertible note	39	48

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Consolidated Statements of Operations (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Revenues:
Net product revenues	$ 64,084	$ 65,673
Royalty revenues	5,516	3,310
License revenue	2,265	2,265
Total net revenues	71,865	71,248
Costs and expenses:
Cost of sales	13,484	12,464
Cost of license revenue	159	159
Research and development	12,520	11,025
Selling, general and administrative	48,198	38,745
Total operating expenses	74,361	62,393
Operating (loss) income	(2,496)	8,855
Other expense (net):
Interest and amortization of debt discount expense	(591)	(766)
Interest income	173	129
Total other expense (net)	(418)	(637)
(Loss) income before taxes	(2,914)	8,218
Benefit from (provision for) income taxes	1,775	(372)
Net (loss) income	$ (1,139)	$ 7,846
Net (loss) income per share-basic (in dollars per share)	$ (0.03)	$ 0.20
Net (loss) income per share-diluted (in dollars per share)	$ (0.03)	$ 0.19
Weighted average common shares outstanding used in computing net (loss) income per share-basic (in shares)	39,832	39,340
Weighted average common shares outstanding used in computing net (loss) income per share-diluted (in shares)	39,832	40,407

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Fair Value Measurements

3 Months Ended

Mar. 31, 2013

Fair Value Measurements

Fair Value Measurements

(6) Fair Value Measurements

The following table presents information about the Company’s assets and liabilities measured at fair value on a recurring basis as of March 31, 2013 and indicates the fair value hierarchy of the valuation techniques utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability. The Company’s Level 1 assets consist of time deposits and investments in a Treasury money market fund and the Company’s Level 2 assets consist of high-quality government bonds and are valued using market prices on the active markets.  Level 1 instrument valuations are obtained from real-time quotes for transactions in active exchange markets involving identical assets and Level 2 assets are valued using quoted prices for similar assets and liabilities in active markets or other market observable inputs such as interest rates and yield curves. The Company’s Level 3 liability represents our put/call liability related to the Paul Royalty Fund (PRF) transaction. No changes in valuation techniques or inputs occurred during the three months ended March 31, 2013.

(In thousands)	Level 1		Level 2		Level 3
March 31, 2013
Assets Carried at Fair Value:
Cash equivalents	$	16,294	$	—	$	—
Short-term investments	—		248,659		—
Long-term investments	—		41,559		—
Liabilities Carried at Fair Value:
Put/call liability	—		—		247
December 31, 2012
Assets Carried at Fair Value:
Cash equivalents	$	27,932	$	—	$	—
Short-term investments	—		191,949		—
Long-term investments	—		99,363		—
Liabilities Carried at Fair Value:
Put/call liability	—		—		329

The following table presents additional information about assets and/or liabilities measured at fair value on a recurring basis and for which the Company utilizes Level 3 inputs to determine fair value.

(In thousands)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Put/call liability:
Balance, beginning of period	$	329		$	1,030
Total realized and unrealized gains included in selling, general and administrative expenses:	(82		)	(535		)
Balance, end of period	$	247		$	495

The Company estimates the fair value of its put/call liability using a discounted cash flow valuation technique. Using this approach, historical and expected future cash flows are calculated over the expected life of the PRF agreement, are discounted, and then exercise scenario probabilities are applied. Some of the more significant assumptions made in the valuation include (i) the estimated Zanaflex revenue forecast and (ii) the likelihood of put/call exercise trigger events such as bankruptcy and change of control. The valuation is performed periodically when the significant assumptions change.  Realized gains and losses are included in selling, general and administrative expenses.

The put/call liability has been classified as a Level 3 liability as its valuation requires substantial judgment and estimation of factors that are not currently observable in the market due to the lack of trading in the security. If different assumptions were used for the various inputs to the valuation approach including, but not limited to, assumptions involving the estimated Zanaflex revenue forecast and the likelihood of trigger events, the estimated fair value could be significantly higher or lower than the fair value we determined. The Company may be required to record losses in future periods, which may be significant.

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Income Taxes

3 Months Ended

Mar. 31, 2013

Income Taxes

Income Taxes

(5) Income Taxes

             For the three-month periods ended March 31, 2013 and 2012, the Company recorded a $1.8 million benefit from and a $372,000 provision for income taxes, respectively, based upon its estimated tax liability for the year. The benefit / provision for income taxes is based on federal, state and Puerto Rico income taxes. The effective income tax rates for the Company for the three-month periods ended March 31, 2013 and 2012 were (60.9)% and 4.5%, respectively. The effective tax rate for the three-month period ended March 31, 2013 benefited from the Company's loss during the three-month period ending March 31, 2013. In addition, as a result of the January 2013 extension of the Federal research and development tax credit retroactive to January 2012 the Company recorded a benefit of $1.2 million for the estimated 2012 credit. During the three-month period ended March 31, 2013 the Company also settled an IRS examination of their corporate income tax returns for years ending December 31, 2009 through December 31, 2011.  The impact of the settlement partially offset the benefit recorded for the research and development tax credit.

                The Company continues to evaluate the realizability of its deferred tax assets and liabilities on a periodic basis and will adjust such amounts in light of changing facts and circumstances including, but not limited to, future projections of taxable income, tax legislation, rulings by relevant tax authorities, the progress of ongoing tax audits and the regulatory approval of products currently under development. Any changes to the valuation allowance or deferred tax assets in the future would impact the Company's income taxes.

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Share-based Compensation (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Share-based compensation expense
Share-based compensation expense recognized	$ 4,933	$ 4,191
Weighted average fair value of options granted to employees (in dollars per share)	$ 15.41	$ 14.15
Research and development
Share-based compensation expense
Share-based compensation expense recognized	1,151	989
Selling, general, and administrative
Share-based compensation expense
Share-based compensation expense recognized	$ 3,782	$ 3,202

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Fair Value Measurements (Tables)

3 Months Ended

Mar. 31, 2013

Fair Value Measurements

Schedule of assets and liabilities measured at fair value on a recurring basis

(In thousands)	Level 1		Level 2		Level 3
March 31, 2013
Assets Carried at Fair Value:
Cash equivalents	$	16,294	$	—	$	—
Short-term investments	—		248,659		—
Long-term investments	—		41,559		—
Liabilities Carried at Fair Value:
Put/call liability	—		—		247
December 31, 2012
Assets Carried at Fair Value:
Cash equivalents	$	27,932	$	—	$	—
Short-term investments	—		191,949		—
Long-term investments	—		99,363		—
Liabilities Carried at Fair Value:
Put/call liability	—		—		329

Schedule of assets and liabilities measured at fair value on a recurring basis utilizing Level 3 inputs

(In thousands)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Put/call liability:
Balance, beginning of period	$	329		$	1,030
Total realized and unrealized gains included in selling, general and administrative expenses:	(82		)	(535		)
Balance, end of period	$	247		$	495

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Commitments and Contingencies

3 Months Ended

Mar. 31, 2013

Commitments and Contingencies

Commitments and Contingencies

(9) Commitments and Contingencies

A summary of the Company’s commitments and contingencies was included in the Company’s Annual Report on Form 10-K for the twelve-month period ended December 31, 2012. The Company’s long-term contractual obligations include commitments and estimated purchase obligations entered into in the normal course of business.

The Company accrues for amounts related to legal matters if it is probable that a liability has been incurred and the amount is reasonably estimable. While losses, if any, are possible the Company is not able to estimate any ranges of losses as of March 31, 2013. Litigation expenses are expensed as incurred.

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Investments

3 Months Ended

Mar. 31, 2013

Investments

Investments

(7) Investments

The Company has determined that all of its investments are classified as available-for-sale. Available-for-sale securities are carried at fair value with interest on these securities included in interest income and are recorded based primarily on quoted market prices. Available-for-sale securities consisted of the following:

(In thousands)	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Estimated fair value
March 31, 2013
US Treasury bonds	$	290,081	$	137	$	—		$	290,218
December 31, 2012
US Treasury bonds	291,209		104		(1		)	291,312

The contractual maturities of short-term available-for-sale debt securities at March 31, 2013 and December 31, 2012 are greater than 3 months but less than 1 year. The contractual and intended maturities of long-term available-for-sale debt securities at March 31, 2013 and December 31, 2012 are greater than 1 year and up to 15 months. The Company has determined that there were no other-than-temporary declines in the fair values of its investments as of March 31, 2013.

Short-term investments with maturity of three months or less from date of purchase have been classified as cash equivalents, and amounted to $16.3 million and $27.9 million as of March 31, 2013 and December 31, 2012, respectively.

The Company holds available-for-sale investment securities which are reported at fair value on the Company’s balance sheet. Unrealized holding gains and losses are reported within accumulated other comprehensive income (AOCI) in the statements of comprehensive (loss) income.  The changes in AOCI associated with the unrealized holding gain on available-for-sale investments during the three months ended March 31, 2013, were as follows (in thousands):

(In thousands)	Net Unrealized Gains (Losses) on Marketable Securities		Total
Balance at December 31, 2012	$	62	$	62
Other comprehensive income before reclassifications:	21		21
Amounts reclassified from accumulated other comprehensive income	—		—
Net current period other comprehensive income	21		21
Balance at March 31, 2013	$	83	$	83

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Collaborations, Alliances, and Other Agreements

3 Months Ended

Mar. 31, 2013

Collaborations, Alliances, and Other Agreements

Collaborations, Alliances, and Other Agreements

(8) Collaborations, Alliances, and Other Agreements

Biogen

On June 30, 2009, the Company entered into an exclusive collaboration and license agreement with Biogen Idec International GmbH (Biogen Idec) to develop and commercialize Ampyra (known as Fampyra outside the U.S.) in markets outside the United States (the “Collaboration Agreement”). Under the Collaboration Agreement, Biogen Idec was granted the exclusive right to commercialize Ampyra and other products containing aminopyridines developed under that agreement in all countries outside of the United States, which grant includes a sublicense of the Company’s rights under an existing license agreement between the Company and Alkermes plc (Alkermes), formerly Elan Corporation, plc (Elan). Biogen Idec has responsibility for regulatory activities and future clinical development of Fampyra in ex-U.S. markets worldwide. The Company also entered into a related supply agreement with Biogen Idec (the “Supply Agreement”), pursuant to which the Company will supply Biogen Idec with its requirements for the licensed products through the Company’s existing supply agreement with Alkermes.

Under the Collaboration Agreement, the Company was entitled to an upfront payment of $110.0 million as of June 30, 2009, which was received in July 2009, and a $25 million milestone payment upon approval of the product in the European Union, which was received in August 2011. The Company is also entitled to receive additional payments of up to $10 million based on the successful achievement of future regulatory milestones and up to $365 million based on the successful achievement of future sales milestones. Due to the uncertainty surrounding the achievement of the future regulatory and sales milestones, these payments will not be recognized as revenue unless and until they are earned. The Company is not able to reasonably predict if and when the milestones will be achieved. Under the Collaboration Agreement, Biogen Idec will be required to make double-digit tiered royalty payments to the Company on ex-U.S. sales. In addition, the consideration that Biogen Idec will pay for licensed products under the Supply Agreement will reflect the price owed to the Company’s suppliers under its supply arrangements with Alkermes or other suppliers for ex-U.S. sales. The Company and Biogen Idec may also carry out future joint development activities regarding licensed product under a cost-sharing arrangement. Under the terms of the Collaboration Agreement, the Company, in part through its participation in joint committees with Biogen Idec, will participate in overseeing the development and commercialization of Ampyra and other licensed products in markets outside the United States pursuant to that agreement. Acorda will continue to develop and commercialize Ampyra independently in the United States.

As of June 30, 2009, the Company recorded a license receivable and deferred revenue of $110.0 million for the upfront payment due to the Company from Biogen Idec under the Collaboration Agreement. Also, as a result of such payment to Acorda, a payment of $7.7 million became payable by Acorda to Alkermes and was recorded as a cost of license payable and deferred expense. The payment of $110.0 million was received from Biogen Idec on July 1, 2009 and the payment of $7.7 million was made to Alkermes on July 7, 2009.

The Company considered the following deliverables with respect to the revenue recognition of the $110.0 million upfront payment:  (1) the license to use the Company’s technology, (2) the Collaboration Agreement to develop and commercialize licensed product in all countries outside the U.S., and (3) the Supply Agreement. Due to the inherent uncertainty in obtaining regulatory approval, the applicability of the Supply Agreement is outside the control of the Company and Biogen Idec. Accordingly, the Company has determined the Supply Agreement is a contingent deliverable at the onset of the agreement.  As a result, the Company has determined the Supply Agreement does not meet the definition of a deliverable that needs to be accounted for at the inception of the arrangement. The Company has also determined that there is no significant and incremental discount related to the supply agreement since Biogen Idec will pay the same amount for inventory that the Company would pay and the Company effectively acts as a middle man in the arrangement for which it adds no significant value due to various factors such as the Company does not have any manufacturing capabilities or other knowhow with respect to the manufacturing process.

The Company has determined that the identified non-contingent deliverables (deliverables 1 and 2 immediately preceding) would have no value on a standalone basis if they were sold separately by a vendor and the customer could not resell the delivered items on a standalone basis, nor does the Company have objective and reliable evidence of fair value for the deliverables. Accordingly, the non-contingent deliverables are treated as one unit of accounting.  As a result, the Company will recognize the non-refundable upfront payment from Biogen Idec as revenue and the associated payment to Alkermes as expense ratably over the estimated term of regulatory exclusivity for the licensed products under the Collaboration Agreement as the Company had determined this was the most probable expected benefit period. The Company recognized $2.3 million in license revenue, a portion of the $110.0 million received from Biogen Idec, and $159,000 in cost of license revenue, a portion of the $7.7 million paid to Alkermes, during the three-month periods ended March 31, 2013 and 2012.

On January 21, 2011 Biogen Idec announced that the European Medicines Agency’s (EMA) Committee for Medicinal Products for Human Use (CHMP) decided against approval of Fampyra to improve walking ability in adult patients with multiple sclerosis.  Biogen Idec, working closely with the Company, filed a formal appeal of the decision.  In May 2011, the CHMP recommended conditional marketing authorization, and in July 2011 Biogen Idec received conditional approval from the European Commission for, Fampyra (prolonged-release fampridine tablets) for the improvement of walking in adult patients with MS with walking disability (Expanded Disability Status Scale of 4-7). The Company currently estimates the recognition period to be approximately 12 years from the date of the Collaboration Agreement. As part of its ex-U.S. license agreement, Biogen Idec owes Acorda royalties based on ex-U.S. net sales, and milestones based on ex-U.S. regulatory approval, new indications, and ex-U.S. net sales.  These milestones included a $25 million payment for approval of the product in the European Union which was recorded and paid in the three month period ended March 31, 2012. Based on Acorda’s worldwide license and supply agreement with Alkermes, Alkermes received 7% of this milestone payment from Acorda during the same period.  For revenue recognition purposes, the Company determined this milestone to be substantive in accordance with applicable accounting guidance related to milestone revenue.  Substantive uncertainty existed at the inception of the arrangement as to whether the milestone would be achieved because of the numerous variables, such as the high rate of failure inherent in the research and development of new products and the uncertainty involved with obtaining regulatory approval. Biogen Idec leveraged Acorda’s U.S. Ampyra study results that contributed to the regulatory approval process. Therefore, the milestone was achieved based in part on Acorda’s past performance.  The milestone was also reasonable relative to all deliverable and payment terms of the collaboration arrangement. Therefore, the payment was recognized in its entirety as revenue and the cost of the milestone revenue was recognized in its entirety as an expense during the three-month period ended March 31, 2012.

Actavis/Watson

The Company has an agreement with Watson Pharma, Inc., a subsidiary of Actavis, Inc. (formerly Watson Pharmaceuticals, Inc.), to market tizanidine hydrochloride capsules, an authorized generic version of Zanaflex Capsules, which was launched in February 2012.  In accordance with the Watson agreement, the Company receives a royalty based on Watson’s gross margin, as defined by the agreement, of the authorized generic product. During the three-month periods ended March 31, 2013 and 2012, the Company recognized royalty revenue of $2.6 million and $1.5 million, respectively, related to the gross margin of the Zanaflex Capsule authorized generic.  During the three-month periods ended March 31, 2013 and 2012, the Company also recognized revenue and a corresponding cost of sales of $493,000 and $1.1 million, respectively, related to the purchase and sale of the related Zanaflex Capsule authorized generic product to Watson, which is recorded in net product revenues and cost of sales.

Neuronex

In December 2012, the Company acquired Neuronex, Inc., a privately-held development stage pharmaceutical company (Neuronex).  Neuronex is developing Diazepam Nasal Spray under Section 505(b)(2) of the Food, Drug and Cosmetic Act as an acute treatment for selected, refractory patients with epilepsy, on stable regimens of antiepileptic drugs, or AEDs, who require intermittent use of diazepam to control bouts of increased seizure activity also known as cluster or acute repetitive seizures, or ARS.

Under the terms of the agreement, the Company made an upfront payment of $2.0 million in February 2012.  The Company also paid $1.5 million during the twelve month period ended December 31, 2012 pursuant to a commitment under the agreement to fund research to prepare for the Diazepam Nasal Spray pre-NDA meeting with the FDA.  In December 2012, the Company completed the acquisition by paying $6.8 million to former Neuronex shareholders less a $300,000 holdback provision to be settled in December 2013.

The former equity holders of Neuronex are entitled to receive from Acorda up to an additional $18 million in contingent earnout payments upon the achievement of specified regulatory and manufacturing-related milestones with respect to the Diazepam Nasal Spray product, and up to $105 million upon the achievement of specified sales milestones with respect to the Diazepam Nasal Spray product.  The former equity holders of Neuronex will also be entitled to receive tiered royalty-like earnout payments, ranging from the upper single digits to lower double digits, on worldwide net sales of Diazepam Nasal Spray products.  These payments are payable on a country-by-country basis until the earlier to occur of ten years after the first commercial sale of a product in such country and the entry of generic competition in such country as defined in the Agreement.

The patent and other intellectual property and other rights relating to the Diazepam Nasal Spray product are licensed from SK Biopharmaceuticals Co., Ltd. (SK).  Pursuant to the SK license, which granted worldwide rights to Neuronex, except certain specified Asian countries, the Company’s subsidiary Neuronex is obligated to pay SK up to $8 million upon the achievement of specified development milestones with respect to the Diazepam Nasal Spray product and up to $3 million upon the achievement of specified sales milestones with respect to the Diazepam Nasal Spray product.  Also, Neuronex is obligated to pay SK a tiered, mid-single digit royalty on net sales of Diazepam Nasal Spray products.

The Company evaluated the transaction based upon the guidance of ASC 805, Business Combinations, and concluded that it will only acquire inputs and did not acquire any processes.  The Company will need to develop its own processes in order to produce an output. Therefore the Company accounted for the transaction as an asset acquisition and accordingly the $2.0 million upfront payment, $1.5 million in research funding and $6.8 million of closing consideration net of tangible net assets acquired of $3.7, million which were primarily the taxable amount of net operating loss carryforwards, were expensed as research and development expense during the twelve-month period ended December 31, 2012.

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Summary of Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2013

Summary of Significant Accounting Policies

Principles of Consolidation

Principles of Consolidation

The accompanying consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States of America and include the results of operations of the Company and its majority owned subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

Use of Estimates

The preparation of the consolidated financial statements requires management of the Company to make a number of estimates and assumptions relating to the reported amount of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the period. Significant items subject to such estimates and assumptions include share-based compensation accounting, which are largely dependent on the fair value of the Company’s equity securities. In addition, the Company recognizes Zanaflex revenue based on estimated prescriptions filled. The Company adjusts its Zanaflex inventory value based on an estimate of inventory that may be returned. Actual results could differ from those estimates.

Investments

Investments

Both short-term and long-term investments consist of US Treasury bonds. The Company classifies marketable securities available to fund current operations as short-term investments in current assets on its consolidated balance sheets. Marketable securities are classified as long-term investments in long-term assets on the consolidated balance sheets if the Company has the ability and intent to hold them and such holding period is longer than one year. The Company classifies its short-term and long-term investments as available-for-sale. Available-for-sale securities are recorded at fair value of the investments based on quoted market prices.

Unrealized holding gains and losses on available-for-sale securities, which are determined to be temporary, are excluded from earnings and are reported as a separate component of accumulated other comprehensive income (loss).

Premiums and discounts on investments are amortized over the life of the related available-for-sale security as an adjustment to yield using the effective-interest method. Dividend and interest income are recognized when earned. Amortized premiums and discounts, dividend and interest income and realized gains and losses are included in interest income.

Accumulated Other Comprehensive Income

Accumulated Other Comprehensive Income

The Company’s accumulated other comprehensive income is comprised of gains and losses on available for sale securities and is recorded and presented net of income tax.

Revenue Recognition

Revenue Recognition

Ampyra

                Ampyra is available only through a network of specialty pharmacy providers that provide the medication to patients by mail; Kaiser Permanente (Kaiser), which distributes Ampyra to patients through a closed network of on-site pharmacies; and ASD Specialty Healthcare, Inc. (an AmerisourceBergen affiliate), which is the exclusive specialty pharmacy distributor for Ampyra to the U.S. Bureau of Prisons and the U.S. Department of Veterans Affairs (VA). Ampyra is not available in retail pharmacies. The Company does not recognize revenue from product sales until there is persuasive evidence of an arrangement, delivery has occurred, the price is fixed and determinable, the buyer is obligated to pay the Company, the obligation to pay is not contingent on resale of the product, the buyer has economic substance apart from the Company, the Company has no obligation to bring about the sale of the product, and the amount of returns can be reasonably estimated and collectability is reasonably assured. The Company recognizes product sales of Ampyra following shipment of product to a network of specialty pharmacy providers, Kaiser, and the specialty distributor to the VA. The specialty pharmacy providers, Kaiser, and the specialty distributor to the VA are contractually obligated to hold no more than an agreed number of days of inventory, ranging from 10 to 30 days.

                The Company’s net revenues represent total revenues less allowances for customer credits, including estimated rebates, discounts and returns. These allowances are recorded for cash consideration given by a vendor to a customer that is presumed to be a reduction of the selling prices of the vendor’s products or services and, therefore, are characterized as a reduction of revenue. At the time product is shipped to specialty pharmacies, Kaiser and the specialty distributor to the VA, an adjustment is recorded for estimated rebates, discounts and returns. These allowances are established by management as its best estimate based on available information and will be adjusted to reflect known changes in the factors that impact such allowances. Allowances for rebates, discounts and returns are established based on the contractual terms with customers, historical trends, communications with customers and the levels of inventory remaining in the distribution channel, as well as expectations about the market for the product and anticipated introduction of competitive products.  Product shipping and handling costs are included in cost of sales.  Effective December 1, 2012, the Company no longer accepts returns of Ampyra with the exception of product damages that occur during shipping.

Zanaflex

The Company applies the revenue recognition guidance in Accounting Standards Codification (ASC) 605-15-25, which among other criteria requires that future returns can be reasonably estimated in order to recognize revenue. The amount of future tablet returns is uncertain due to generic competition and customer conversion to Zanaflex Capsules. The Company has accumulated some sales history with Zanaflex Capsules; however, due to existing and potential generic competition and customer conversion from Zanaflex tablets to Zanaflex Capsules, we do not believe we can reasonably determine a return rate at this time. As a result, the Company accounts for these product shipments using a deferred revenue recognition model. Under the deferred revenue model, the Company does not recognize revenue upon product shipment. For these product shipments, the Company invoices the wholesaler, records deferred revenue at gross invoice sales price, and classifies the cost basis of the product held by the wholesaler as a component of inventory. The Company recognizes revenue when prescribed to the end-user, on a first-in first-out (FIFO) basis. The Company’s revenue to be recognized is based on (1) the estimated prescription demand, based on pharmacy sales for its products; and (2) the Company’s analysis of third-party information, including third-party market research data. The Company’s estimates are subject to the inherent limitations of estimates that rely on third-party data, as certain third-party information is itself in the form of estimates, and reflect other limitations. The Company’s sales and revenue recognition reflects the Company’s estimates of actual product prescribed to the end-user. The Company expects to be able to apply a more traditional revenue recognition policy such that revenue is recognized following shipment to the customer when it believes it has sufficient data to develop reasonable estimates of expected returns based upon historical returns and greater certainty regarding generic competition.

The Company’s net revenues represent total revenues less allowances for customer credits, including estimated discounts, rebates, and chargebacks. These allowances are recorded for cash consideration given by a vendor to a customer that is presumed to be a reduction of the selling prices of the vendor’s products or services and, therefore, should be characterized as a reduction of revenue when recognized in the vendor’s statement of operations. Adjustments are recorded for estimated chargebacks, rebates, and discounts. These allowances are established by management as its best estimate based on available information and are adjusted to reflect known changes in the factors that impact such allowances. Allowances for chargebacks, rebates and discounts are established based on the contractual terms with customers, analysis of historical levels of discounts, chargebacks and rebates, communications with customers and the levels of inventory remaining in the distribution channel, as well as expectations about the market for each product and anticipated introduction of competitive products. In addition, the Company records a charge to cost of goods sold for the cost basis of the estimated product returns the Company believes may ultimately be realized at the time of product shipment to wholesalers. The Company has recognized this charge at the date of shipment since it is probable that it will receive a level of returned products; upon the return of such product it will be unable to resell the product considering its expiration dating; and it can reasonably estimate a range of returns. This charge represents the cost basis for the low end of the range of the Company’s estimated returns. Product shipping and handling costs are included in cost of sales.

Milestones and royalties

In order to determine the revenue recognition for contingent milestones, the Company evaluates the contingent milestones using the criteria as provided by the Financial Accounting Standards Boards (FASB) guidance on the milestone method of revenue recognition. At the inception of a collaboration agreement the Company evaluates if payments are substantive.  The criteria requires that (i) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from the Company’s activities to achieve the milestone, (ii) the milestone be related to past performance, and (iii) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement.  If these criteria are met then the contingent milestones can be considered substantive milestones and will be recognized as revenue in the period that the milestone is achieved. Royalties are recognized as earned in accordance with the terms of various research and collaboration agreements.

Collaborations

Collaborations

The Company recognizes collaboration revenues and expenses by analyzing each element of the agreement to determine if it shall be accounted for as a separate element or single unit of accounting. If an element shall be treated separately for revenue recognition purposes, the revenue recognition principles most appropriate for that element are applied to determine when revenue shall be recognized. If an element shall not be treated separately for revenue recognition purposes, the revenue recognition principles most appropriate for the bundled group of elements are applied to determine when revenue shall be recognized. Payments received in excess of revenues recognized are recorded as deferred revenue until such time as the revenue recognition criteria have been met.

Concentration of Risk

Concentration of Risk

Financial instruments that potentially subject the Company to concentrations of credit risk consist principally of investments in cash, cash equivalents, restricted cash and accounts receivable. The Company maintains cash, cash equivalents, restricted cash, short-term and long-term investments with approved financial institutions. The Company is exposed to credit risks and liquidity in the event of default by the financial institutions or issuers of investments in excess of FDIC insured limits. The Company performs periodic evaluations of the relative credit standing of these financial institutions and limits the amount of credit exposure with any institution.

Segment Information

Segment Information

                The Company is managed and operated as one business. The entire business is managed by a single management team that reports to the Chief Executive Officer. The Company does not operate separate lines of business with respect to any of its products or product candidates. Accordingly, the Company does not prepare discrete financial information with respect to separate products or product candidates or by location and does not have separately reportable segments.

Subsequent Events

Subsequent Events

                Subsequent events are defined as those events or transactions that occur after the balance sheet date, but before the financial statements are filed with the Securities and Exchange Commission. The Company completed an evaluation of the impact of any subsequent events through the date these financial statements were issued, and determined there were no subsequent events requiring disclosure in or requiring adjustment to these financial statements.

Recent Accounting Pronouncements

Recent Accounting Pronouncements

In February 2013, the FASB amended its guidance to require an entity to present the effect of certain significant reclassifications out of accumulated other comprehensive income on the respective line items in net income. The new accounting guidance does not change the items that must be reported in other comprehensive income or when an item of other comprehensive income must be reclassified to net income. The guidance is effective prospectively for fiscal years beginning after December 15, 2012.  The Company adopted these new provisions for the quarter beginning January 1, 2013. As the guidance requires additional presentation only, there was no impact to the Company’s consolidated results of operations or financial position.

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Summary of Significant Accounting Policies (Details) (Ampyra)	3 Months Ended
	Mar. 31, 2013
Minimum
Revenue Recognition
Contractually obligated inventory holdings period	10 days
Maximum
Revenue Recognition
Contractually obligated inventory holdings period	30 days

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Earnings Per Share (Details 2) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Stock options and restricted common shares
Antidilutive Securities
Anti-dilutive securities excluded from computation of earnings per share	7,540	5,189
Convertible note
Antidilutive Securities
Anti-dilutive securities excluded from computation of earnings per share	39	48

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Consolidated Statements of Comprehensive (Loss) Income (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Consolidated Statements of Comprehensive (Loss) Income
Net (loss) income	$ (1,139)	$ 7,846
Other comprehensive income (loss):
Unrealized gains (losses) on available for sale securities, net of tax	21	(100)
Other comprehensive income (loss), net of tax	21	(100)
Comprehensive (loss) income	$ (1,118)	$ 7,746

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Earnings Per Share

3 Months Ended

Mar. 31, 2013

Earnings Per Share

Earnings Per Share

(4) Earnings Per Share

The following table sets forth the computation of basic and diluted earnings per share for the three-month periods ended March 31, 2013 and 2012:

(In thousands, except per share data)	Three-month period ended March 31, 2013			Three-month period ended March 31, 2012
Basic and diluted
Net (loss) income	$	(1,139	)	$	7,846
Weighted average common shares outstanding used in computing net (loss) income per share—basic	39,832			39,340
Plus: net effect of dilutive stock options and restricted common shares	—			1,067
Weighted average common shares outstanding used in computing net (loss) income per share—diluted	39,832			40,407
Net (loss) income per share—basic	$	(0.03	)	$	0.20
Net (loss) income per share—diluted	$	(0.03	)	$	0.19

The difference between basic and diluted shares is that diluted shares include the dilutive effect of the assumed exercise of outstanding securities. The Company’s stock options and unvested shares of restricted common stock could have the most significant impact on diluted shares.

Securities that could potentially be dilutive are excluded from the computation of diluted earnings per share when a loss from continuing operations exists or when the exercise price exceeds the average closing price of the Company’s common stock during the period, because their inclusion would result in an anti-dilutive effect on per share amounts.

The following amounts were not included in the calculation of net (loss) income per diluted share because their effects were anti-dilutive:

(In thousands)	Three-month period ended March 31, 2013	Three-month period ended March 31, 2012
Denominator
Stock options and restricted common shares	7,540	5,189
Convertible note	39	48

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Income Taxes (Details) (USD $)	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Income Taxes
Income tax benefit (provision)	$ 1,775,000	$ (372,000)
Effective income tax rate (as a percent)	(60.90%)	4.50%
Tax credit	$ 1,200,000

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Investments (Tables)

3 Months Ended

Mar. 31, 2013

Investments

Schedule of available-for-sale securities

(In thousands)	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Estimated fair value
March 31, 2013
US Treasury bonds	$	290,081	$	137	$	—		$	290,218
December 31, 2012
US Treasury bonds	291,209		104		(1		)	291,312

Schedule of changes in accumulated other comprehensive income

(In thousands)	Net Unrealized Gains (Losses) on Marketable Securities		Total
Balance at December 31, 2012	$	62	$	62
Other comprehensive income before reclassifications:	21		21
Amounts reclassified from accumulated other comprehensive income	—		—
Net current period other comprehensive income	21		21
Balance at March 31, 2013	$	83	$	83