Ironwood Pharmaceuticals (IRWD) 10-K 7 Feb 14 2013 FY Annual report Financial data

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
	Dec. 31, 2013	Jun. 30, 2013	Jan. 28, 2014	Jan. 28, 2014
			Class A common stock	Class B common stock
Entity Registrant Name	'IRONWOOD PHARMACEUTICALS INC	'	'	'
Entity Central Index Key	'0001446847	'	'	'
Document Type	'10-K	'	'	'
Document Period End Date	31-Dec-13	'	'	'
Amendment Flag	'false	'	'	'
Current Fiscal Year End Date	'--12-31	'	'	'
Entity Well-known Seasoned Issuer	'Yes	'	'	'
Entity Voluntary Filers	'No	'	'	'
Entity Current Reporting Status	'Yes	'	'	'
Entity Filer Category	'Large Accelerated Filer	'	'	'
Entity Public Float	'	$1,108,219,339	'	'
Entity Common Stock, Shares Outstanding	'	'	103,113,155	18,360,454
Document Fiscal Year Focus	'2013	'	'	'
Document Fiscal Period Focus	'FY	'	'	'

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$75,490	$136,700
Available-for-sale securities	122,112	31,528
Accounts receivable	513	457
Related party accounts receivable, net	2,700	1,030
Inventory	22,145	6,699
Prepaid expenses and other current assets	6,168	8,026
Total current assets	229,128	184,440
Restricted cash	8,147	7,647
Property and equipment, net	37,376	37,537
Other assets	4,311	283
Total assets	278,962	229,907
Current liabilities:	'	'
Accounts payable	10,139	14,217
Related party accounts payable, net	48	7,509
Accrued research and development costs	3,412	5,664
Accrued expenses	18,438	21,171
Current portion of capital lease obligations	1,139	261
Current portion of deferred rent	2,790	2,735
Current portion of deferred revenue	5,074	3,381
Total current liabilities	41,040	54,938
Capital lease obligations, net of current portion	3,134	308
Deferred rent, net of current portion	8,822	11,593
Deferred revenue, net of current portion	11,416	18,024
Notes payable	174,672	'
Other liabilities	1,653	992
Commitments and contingencies (Note 4, 10 and 11)	'	'
Stockholders' equity:	'	'
Preferred stock, $0.001 par value, 75,000,000 shares authorized, no shares issued and outstanding	'	'
Additional paid-in capital	815,930	648,955
Accumulated deficit	-777,828	-505,016
Accumulated other comprehensive income	2	5
Total stockholders' equity	38,225	144,052
Total liabilities and stockholders' equity	278,962	229,907
Class A common stock	'	'
Stockholders' equity:	'	'
Common stock	103	78
Class B common stock	'	'
Stockholders' equity:	'	'
Common stock	$18	$30

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Dec. 31, 2013	Dec. 31, 2012
Preferred stock, par value (in dollars per share)	$0.00	$0.00
Preferred stock, shares authorized	75,000,000	75,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Class A common stock	'	'
Common stock, par value (in dollars per share)	$0.00	$0.00
Common stock, shares authorized	500,000,000	500,000,000
Common stock, shares issued	102,803,093	78,253,074
Common stock, shares outstanding	102,803,093	78,253,074
Class B common stock	'	'
Common stock, par value (in dollars per share)	$0.00	$0.00
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	18,362,037	29,512,253
Common stock, shares outstanding	18,362,037	29,512,253

Consolidated_Statements_of_Ope

Consolidated Statements of Operations (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Consolidated Statements of Operations	'	'	'
Collaborative arrangements revenue	$22,881	$150,245	$65,871
Cost and expenses:	'	'	'
Costs of revenue	7,203	965	'
Research and development	102,378	113,474	86,093
Selling, general and administrative	123,228	92,538	45,920
Collaboration expense	42,074	16,030	'
Total cost and expenses	274,883	223,007	132,013
Loss from operations	-252,002	-72,762	-66,142
Other income (expense):	'	'	'
Interest expense	-21,002	-59	-63
Interest and investment income	192	197	456
Other income	'	'	900
Other income (expense), net	-20,810	138	1,293
Net loss before income tax expense	-272,812	-72,624	-64,849
Income tax expense	'	'	3
Net loss	($272,812)	($72,624)	($64,852)
Net loss per share - basic and diluted (in dollars per share)	($2.35)	($0.68)	($0.65)
Weighted average number of common shares used in net loss per share - basic and diluted: (in shares)	115,852	106,403	99,875

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Loss (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Consolidated Statements of Comprehensive Loss	'	'	'
Net loss	($272,812)	($72,624)	($64,852)
Other comprehensive income (loss):	'	'	'
Unrealized gains (losses) on available-for-sale securities	-3	-1	5
Total other comprehensive income (loss)	-3	-1	5
Comprehensive loss	($272,815)	($72,625)	($64,847)

Consolidated_Statements_of_Sto

Consolidated Statements of Stockholders' Equity (USD $)	Total	Class A common stock	Common Stock	Common Stock	Additional paid-in capital	Accumulated deficit	Accumulated other comprehensive income (loss)
In Thousands, except Share data, unless otherwise specified	USD ($)		Class A common stock	Class B common stock	USD ($)	USD ($)	USD ($)
			USD ($)	USD ($)
Balance at Dec. 31, 2010	$159,551	'	$48	$51	$526,991	($367,540)	$1
Balance (in shares) at Dec. 31, 2010	'	'	48,202,089	50,970,247	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'
Issuance of common stock upon exercise of stock options and employee stock purchase plan	3,393	'	'	2	3,391	'	'
Issuance of common stock upon exercise of stock options and employee stock purchase plan (in shares)	'	'	112,433	1,463,449	'	'	'
Issuance of common stock awards	30	'	'	'	30	'	'
Issuance of common stock awards (in shares)	'	'	2,328	'	'	'	'
Cancellation of restricted common stock awards (in shares)	'	'	'	-27,500	'	'	'
Conversion of Class B common stock to Class A common stock	'	'	14	-14	'	'	'
Conversion of Class B common stock to Class A common stock (in shares)	'	'	13,484,920	-13,484,920	'	'	'
Share-based compensation expense related to issuance of stock options to non-employees	152	'	'	'	152	'	'
Share-based compensation expense related to issuance of stock options to employees and employee stock purchase plan	11,550	'	'	'	11,550	'	'
Repurchase and retirement of shares of common stock (in shares)	'	'	'	-7,196	'	'	'
Restricted common stock no longer subject to repurchase	27	'	'	'	27	'	'
Unrealized gain (loss) on short-term investments	5	'	'	'	'	'	5
Net loss	-64,852	'	'	'	'	-64,852	'
Balance at Dec. 31, 2011	109,856	'	62	39	542,141	-432,392	6
Balance (in shares) at Dec. 31, 2011	'	'	61,801,770	38,914,080	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'
Issuance of common stock upon exercise of stock options and employee stock purchase plan	4,020	'	'	1	4,019	'	'
Issuance of common stock upon exercise of stock options and employee stock purchase plan (in shares)	'	'	226,658	782,955	'	'	'
Issuance of common stock awards	30	'	'	'	30	'	'
Issuance of common stock awards (in shares)	'	'	2,364	'	'	'	'
Issuance of common stock upon public offering, net of offering costs of $7.9 million and $5.9 million for the year ended 2013 and 2012, respectively	85,228	'	6	'	85,222	'	'
Issuance of common stock upon public offering, net of offering costs (in shares)	'	'	6,037,500	'	'	'	'
Conversion of Class B common stock to Class A common stock	'	'	10	-10	'	'	'
Conversion of Class B common stock to Class A common stock (in shares)	'	'	10,184,782	-10,184,782	'	'	'
Share-based compensation expense related to issuance of stock options to non-employees	60	'	'	'	60	'	'
Share-based compensation expense related to issuance of stock options to employees and employee stock purchase plan	17,483	'	'	'	17,483	'	'
Restricted common shares subject to repurchase	-7	'	'	'	-7	'	'
Restricted common stock no longer subject to repurchase	7	'	'	'	7	'	'
Unrealized gain (loss) on short-term investments	-1	'	'	'	'	'	-1
Net loss	-72,624	'	'	'	'	-72,624	'
Balance at Dec. 31, 2012	144,052	'	78	30	648,955	-505,016	5
Balance (in shares) at Dec. 31, 2012	'	'	78,253,074	29,512,253	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'
Issuance of common stock upon exercise of stock options and employee stock purchase plan	9,297	'	1	1	9,295	'	'
Issuance of common stock upon exercise of stock options and employee stock purchase plan (in shares)	'	'	645,196	1,538,887	'	'	'
Issuance of common stock awards	28	'	'	'	28	'	'
Issuance of common stock awards (in shares)	'	'	10,772	'	'	'	'
Issuance of common stock upon public offering, net of offering costs of $7.9 million and $5.9 million for the year ended 2013 and 2012, respectively	137,766	'	11	'	137,755	'	'
Issuance of common stock upon public offering, net of offering costs (in shares)	'	'	11,204,948	'	'	'	'
Conversion of Class B common stock to Class A common stock	'	'	13	-13	'	'	'
Conversion of Class B common stock to Class A common stock (in shares)	'	'	12,689,103	-12,689,103	'	'	'
Share-based compensation expense related to issuance of stock options to non-employees	272	'	'	'	272	'	'
Share-based compensation expense related to issuance of stock options to employees and employee stock purchase plan	19,624	'	'	'	19,624	'	'
Restricted common stock no longer subject to repurchase	1	'	'	'	1	'	'
Unrealized gain (loss) on short-term investments	-3	'	'	'	'	'	-3
Net loss	-272,812	'	'	'	'	-272,812	'
Balance at Dec. 31, 2013	$38,225	'	$103	$18	$815,930	($777,828)	$2
Balance (in shares) at Dec. 31, 2013	'	'	102,803,093	18,362,037	'	'	'

Consolidated_Statements_of_Sto1

Consolidated Statements of Stockholders' Equity (Parenthetical) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Consolidated Statements of Stockholders' Equity	'	'
Issuance of common stock upon public offering, offering costs	$7.90	$5.90

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash flows from operating activities:	'	'	'
Net loss	($272,812)	($72,624)	($64,852)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'	'
Depreciation and amortization	11,729	11,325	9,999
Loss on disposal of property and equipment	610	20	7
Share-based compensation expense	19,829	17,573	11,732
Accretion of discount/premium on investment securities	1,254	1,157	2,234
Non-cash interest expense	1,719	'	'
Changes in assets and liabilities:	'	'	'
Accounts receivable and related party accounts receivable	-1,726	-835	2,243
Restricted cash	-500	'	2,833
Prepaid expenses and other current assets	-52	-5,127	2,421
Inventory	-11,915	-6,699	'
Other assets	116	-145	136
Accounts payable and accrued expenses	-11,724	24,241	5,086
Accrued research and development costs	-2,252	-1,346	-1,130
Deferred revenue	-4,915	-36,016	-45,012
Deferred rent	-2,716	-2,149	-934
Other liabilities	'	992	'
Net cash used in operating activities	-273,355	-69,633	-75,237
Cash flows from investing activities:	'	'	'
Purchases of available-for-sale securities	-287,943	-96,709	-97,511
Sales and maturities of available-for-sale securities	196,102	140,757	222,254
Purchases of property and equipment	-9,592	-13,979	-9,682
Proceeds from sale of property and equipment	'	9	4
Net cash provided by (used in) investing activities	-101,433	30,078	115,065
Cash flows from financing activities:	'	'	'
Proceeds from issuance of common stock	137,766	85,228	'
Proceeds from issuance of notes payable	175,000	'	'
Costs associated with issuance of notes payable	-7,717	'	'
Proceeds from exercise of stock options, stock purchase plan	9,297	4,020	3,393
Payments on capital lease obligations	-768	-275	-260
Net cash provided by financing activities	313,578	88,973	3,133
Net increase (decrease) in cash and cash equivalents	-61,210	49,418	42,961
Cash and cash equivalents, beginning of period	136,700	87,282	44,321
Cash and cash equivalents, end of period	75,490	136,700	87,282
Supplemental cash flow disclosures:	'	'	'
Cash paid for interest	18,428	55	64
Cash paid for income taxes	'	'	3
Purchases under capital leases	$4,472	$247	$325

Nature_of_Business

Nature of Business	12 Months Ended
	Dec. 31, 2013
Nature of Business	'
Nature of Business	'
	1. Nature of Business
	Ironwood Pharmaceuticals, Inc. (the "Company") is an entrepreneurial pharmaceutical company focused on creating medicines that make a difference for patients, building value to earn the continued support of its fellow shareholders, and empowering its team to passionately pursue excellence. The Company's core strategy is to establish a leading gastrointestinal ("GI") therapeutics company, leveraging its development and commercial capabilities in addressing GI disorders as well as its pharmacologic expertise in guanylate cyclase ("GC") pathways.
	The Company's lead product, linaclotide, is being marketed in the United States ("U.S.") under the trademarked name of LINZESS®. In August 2012, the United States Food and Drug Administration ("FDA") approved LINZESS as a once-daily treatment for adult men and women suffering from irritable bowel syndrome with constipation ("IBS-C") or chronic idiopathic constipation ("CIC"). LINZESS is the first and, to date, only FDA-approved guanylate cyclase type-C ("GC-C") agonist. The Company and its collaboration partner, Forest Laboratories, Inc. ("Forest"), began commercializing LINZESS in December 2012.
	In November 2012, the European Commission granted marketing authorization to linaclotide (CONSTELLA®) for the symptomatic treatment of moderate to severe IBS-C in adults. CONSTELLA is the first and only drug approved in the European Union ("E.U.") for IBS-C. The Company's European partner, Almirall, S.A. ("Almirall"), has exclusive marketing rights for CONSTELLA in Europe (including the Commonwealth of Independent States and Turkey). Currently, CONSTELLA is commercially available in certain European countries, including the United Kingdom and Germany.
	In December 2013, the Health Canada granted approval of CONSTELLA as a once-daily, first-in-class treatment for adult women and men suffering from IBS-C or CIC. Forest has exclusive rights to develop and commercialize linaclotide in Canada.
	Astellas Pharma Inc. ("Astellas"), the Company's partner in Japan, is developing linaclotide for the treatment of patients with IBS-C in its territory. Astellas recently completed a double-blind, placebo-controlled, dose-ranging Phase II clinical trial of linaclotide in adult patients with IBS-C. In February 2014, the Company received preliminary top level data for the Phase II trial from Astellas indicating that, while all linaclotide dose groups showed numerically higher responder rates in the primary endpoint than placebo, the responder rates were not statistically significant compared to placebo in this study. Linaclotide was well tolerated in all dose groups in this study. Data analysis is still ongoing at Astellas to determine next steps.
	In October 2012, the Company entered into a collaboration agreement with AstraZeneca AB ("AstraZeneca") to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau, with AstraZeneca having primary responsibility for the local operational execution. In the third quarter of 2013, the Company and AstraZeneca initiated a double-blind, placebo-controlled Phase III clinical trial of linaclotide in adult patients with IBS-C.
	The Company continues to assess alternatives to bring linaclotide to IBS-C and CIC sufferers in the parts of the world outside of its partnered territories.
	The Company is also exploring development opportunities to enhance the clinical profile of LINZESS by seeking to expand its utility in its indicated populations, as well as studying linaclotide in additional indications and populations, new formulations and in combination with other products to assess its potential to treat various GI conditions. In addition to linaclotide-based opportunities, the Company is advancing multiple GI development programs as well as further leveraging its GC expertise to advance a second GC program targeting soluble guanylate cyclase, a validated mechanism with the potential for broad therapeutic utility and multiple opportunities for product development.
	The Company was incorporated in Delaware on January 5, 1998 as Microbia, Inc. On April 7, 2008, the Company changed its name to Ironwood Pharmaceuticals, Inc. To date, the Company has dedicated substantially all of its activities to the research, development and commercialization of linaclotide, the Company's lead product and product candidate, as well as research and development of other product candidates. The Company has incurred significant operating losses since its inception in 1998. As of December 31, 2013, the Company had an accumulated deficit of $777.8 million.

Summary_of_Significant_Account

Summary of Significant Accounting Policies

12 Months Ended

Dec. 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 include the accounts of Ironwood Pharmaceuticals, Inc. and its wholly owned subsidiaries, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. All intercompany transactions and balances are eliminated in consolidation.

Use of Estimates

The preparation of consolidated financial statements in accordance with generally accepted accounting principles in the U.S. requires the Company's management to make estimates and judgments that may affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities. On an on-going basis, the Company's management evaluates its estimates, including those related to revenue recognition, available-for-sale securities, inventory valuation and related reserves, impairment of long-lived assets, balance sheet classification of notes payable, income taxes including the valuation allowance for deferred tax assets, research and development expense, contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

Cash and Cash Equivalents

The Company considers all highly liquid investment instruments with a remaining maturity when purchased of three months or less to be cash equivalents. Investments qualifying as cash equivalents primarily consist of money market funds and U.S. government-sponsored securities. The carrying amount of cash equivalents approximates fair value. The amount of cash equivalents included in cash and cash equivalents was approximately $67.3 million and approximately $113.9 million at December 31, 2013 and 2012, respectively.

Restricted Cash

The Company is contingently liable under unused letters of credit with a bank, related to the Company's facility and automobile lease agreements and credit card arrangements, in the amount of approximately $8.1 million and approximately $7.6 million as of December 31, 2013 and 2012, respectively. As a result, the Company has restricted cash of approximately $8.1 million and approximately $7.6 million as of December 31, 2013 and 2012, respectively, securing these letters of credit. The cash will be restricted until the termination of the leases and credit card arrangements.

Available-for-Sale Securities

The Company classifies all short-term investments with a remaining maturity when purchased of greater than three months as available-for-sale. Available-for-sale securities are recorded at fair value, with the unrealized gains and losses reported in other comprehensive income (loss). The amortized cost of debt securities in this category is adjusted for the amortization of premiums and accretion of discounts to maturity. Such amortization is included in interest and investment income. Realized gains and losses, interest, dividends, and declines in value judged to be other than temporary on available-for-sale securities are included in interest and investment income.

The cost of securities sold is based on the specific identification method for purposes of recording realized gains and losses. To determine whether an other-than-temporary impairment exists, the Company considers whether it has the ability and intent to hold the investment until a market price recovery, and whether evidence indicating the recoverability of the cost of the investment outweighs evidence to the contrary. There were no other-than-temporary impairments for the years ended December 31, 2013, 2012 and 2011.

Inventory

Inventory is stated at the lower of cost or market with cost determined under the first-in, first-out basis.

The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements or inventory that fails to meet commercial sale specifications is written down with a corresponding charge to cost of revenue in the period that the impairment is first identified.

The Company capitalizes inventories manufactured in preparation for initiating sales of a product candidate when the related product candidate is considered to have a high likelihood of regulatory approval and the related costs are expected to be recoverable through sales of the inventories. In determining whether or not to capitalize such inventories, the Company evaluates, among other factors, information regarding the product candidate's safety and efficacy, the status of regulatory submissions and communications with regulatory authorities and the outlook for commercial sales, including the existence of current or anticipated competitive drugs and the availability of reimbursement. In addition, the Company evaluates risks associated with manufacturing the product candidate, including the ability of the Company's third-party suppliers to complete the validation batches, and the remaining shelf life of the inventories.

Costs associated with developmental products prior to satisfying the inventory capitalization criteria are charged to research and development expense as incurred.

Concentrations of Suppliers

The Company relies on third-party manufacturers and its collaboration partners to manufacture the linaclotide active pharmaceutical ingredient ("API") and final linaclotide drug product. Currently, there are two third-party manufacturers approved for the production of the linaclotide API in three facilities. The Company's collaboration partners, except AstraZeneca in China, (Forest, Almirall and Astellas) are responsible for drug product manufacturing of linaclotide into finished product for their respective territories. The Company also has an agreement with another independent third party to serve as a second source of drug product manufacturing of linaclotide for its partnered territories. The Company and AstraZeneca also continue to explore manufacturing alternatives for China. If any of the Company's suppliers were to limit or terminate production or otherwise fail to meet the quality or delivery requirements needed to satisfy the supply commitments, the process of locating and qualifying alternate sources could require up to several months, during which time the Company's production could be delayed. Such delays could have a material adverse effect on the Company's business, financial position and results of operations.

Accounts Receivable and Related Valuation Account

The Company makes judgments as to its ability to collect outstanding receivables and provides an allowance for receivables when collection becomes doubtful. Provisions are made based upon a specific review of all significant outstanding invoices and the overall quality and age of those invoices not specifically reviewed. The Company's receivables primarily relate to amounts reimbursed under its collaboration and license agreements. The Company believes that credit risks associated with these collaborators are not significant. To date, the Company has not had any write-offs of bad debt, and as such, the Company does not have an allowance for doubtful accounts as of December 31, 2013 and 2012.

Concentrations of Credit Risk

Financial instruments that subject the Company to credit risk primarily consist of cash and cash equivalents, restricted cash, available-for-sale securities, and accounts receivable. The Company maintains its cash and cash equivalent balances with high-quality financial institutions and, consequently, the Company believes that such funds are subject to minimal credit risk. The Company's available-for-sale investments primarily consist of U.S. Treasury securities and certain U.S. government sponsored securities and potentially subject the Company to concentrations of credit risk. The Company has adopted an investment policy which limits the amounts the Company may invest in any one type of investment, and requires all investments held by the Company to be at least A+ rated, thereby reducing credit risk exposure.

Accounts receivable, including related party accounts receivable, primarily consist of amounts due under the collaboration agreement with Forest and license agreement with Astellas (Note 4) for which the Company does not obtain collateral. Accounts receivable or payable to or from Forest and Almirall are presented as related party transactions on the consolidated balance sheets as both entities own common stock of the Company.

The percentages of revenue recognized from significant customers of the Company in the years ended December 31, 2013, 2012 and 2011 as well as the account receivable balances, net of any payables due, at December 31, 2013 and 2012 are included in the following table:

Accounts Receivable

Revenue

December 31,

Years Ended December 31,

2013

2012

2013

2012

2011

Collaborative Partner:

Forest

84

%

—

%

13

%

67

%

64

%

Almirall

—

%

69

%

57

%

14

%

31

%

Astellas

16

%

31

%

25

%

3

%

5

%

AstraZeneca

—

%

—

%

5

%

16

%

—

%

As of December 31, 2013, the Company was in a net payable position with AstraZeneca; as such, there was no accounts receivable due from AstraZeneca as of December 31, 2013. As of December 31, 2012, the Company was in a net payable position with Forest; as such, there was no accounts receivable due from Forest as of December 31, 2012.

For the years ended December 31, 2013, 2012 and 2011, no additional customers accounted for more than 10% of the Company's revenue.

Revenue Recognition

The Company's revenue is generated through collaborative research and development and licensing agreements. The terms of these agreements contain multiple deliverables which may include (i) licenses, (ii) research and development activities, including participation on joint steering committees, and (iii) the manufacture of finished drug product, API, or development materials for the collaborative partner which are reimbursed at a contractually determined rate. Non-refundable payments to the Company under these agreements may include (i) up-front license fees, (ii) payments for research and development activities, (iii) payments for the manufacture of finished drug product, API, or development materials, (iv) payments based upon the achievement of certain milestones, and (v) royalties on product sales. Additionally, the Company may receive its share of the net profits or bear its share of the net losses from the sale of linaclotide in the U.S. and China through its collaborations with Forest and AstraZeneca, respectively.

At December 31, 2013, the Company had collaboration agreements with Forest and AstraZeneca and license agreements with Almirall and Astellas. Refer to Note 4, "Collaboration and License Agreements," for additional discussion of these agreements.

The Company recognizes revenue when there is persuasive evidence that an arrangement exists, services have been rendered or delivery has occurred, the price is fixed or determinable, and collection is reasonably assured.

For certain of our arrangements, particularly the license agreement with Almirall, it is required that taxes be withheld on payments to the Company. The Company has adopted a policy to recognize revenue net of these tax withholdings.

Agreements Entered into Prior to January 1, 2011

For arrangements that include multiple deliverables, the Company follows the provisions of the Accounting Standards Codification ("ASC") Topic 605-25, Revenue Recognition—Multiple-Element Arrangements ("ASC 605-25"), in accounting for these agreements. Under ASC 605-25, the Company was required to identify the deliverables included within the agreement and evaluate which deliverables represent separate units of accounting. Collaborative research and development and licensing agreements that contained multiple deliverables were divided into separate units of accounting when the following criteria were met:

•

Delivered element(s) had value to the collaborator on a standalone basis,

•

There was objective and reliable evidence of the fair value of the undelivered obligation(s), and

•

If the arrangement included a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) was considered probable and substantially within the Company's control.

The Company allocated arrangement consideration among the separate units of accounting either on the basis of each unit's respective fair value or using the residual method, and applied the applicable revenue recognition criteria to each of the separate units. If the separation criteria were not met, revenue of the combined unit of accounting was recorded based on the method appropriate for the last delivered item.

Up-Front License Fees

The Company recognizes revenue from nonrefundable, up-front license fees on a straight-line basis over the contracted or estimated period of performance, which is typically the period over which the research and development is expected to occur or manufacturing services are expected to be provided. Accordingly, the Company is required to make estimates regarding the drug development and commercialization timelines for drugs and drug candidates being developed pursuant to the applicable agreement. The determination of the length of the period over which to recognize the revenue is subject to judgment and estimation and can have an impact on the amount of revenue recognized in a given period. Quarterly, the Company reassesses its period of substantial involvement over which the Company amortizes its up-front license fees and makes adjustments as appropriate. The Company's estimates regarding the period of performance under its collaborative research and development and licensing agreements have changed in the past and may change in the future. In the event that a license were to be terminated, the Company would recognize as revenue any portion of the up-front fee that had not previously been recorded as revenue, but was classified as deferred revenue at the date of such termination. At December 31, 2013, only a portion of Astellas' up-front license fee remains deferred as the period of performance under the Forest and Almirall arrangements ended in the quarter ended September 30, 2012.

Agreements Entered into or Materially Modified on or after January 1, 2011

The Company evaluates revenue from new multiple element agreements entered into on or after January 1, 2011 under ASU No. 2009-13, Multiple-Deliverable Revenue Arrangements ("ASU 2009-13"), which was adopted on a prospective basis in January 2011. The Company also evaluates whether amendments to its multiple element arrangements are considered material modifications that are subject to the application of ASU 2009-13. This evaluation requires management to assess all relevant facts and circumstances and to make subjective determinations and judgments. As part of this assessment, the Company considers whether the modification results in a material change to the arrangement, including whether there is a change in total arrangement consideration that is more than insignificant, whether there are changes in the deliverables included in the arrangement, whether there is a change in the term of the arrangement and whether there is a significant modification to the delivery schedule for contracted deliverables.

When evaluating multiple element arrangements under ASU 2009-13, the Company considers whether the deliverables under the arrangement represent separate units of accounting. This evaluation requires subjective determinations and requires management to make judgments about the individual deliverables and whether such deliverables are separable from the other aspects of the contractual relationship. In determining the units of accounting, management evaluates certain criteria, including whether the deliverables have standalone value, based on the consideration of the relevant facts and circumstances for each arrangement. Factors considered in this determination include the research, manufacturing and commercialization capabilities of the partner and the availability of peptide research and manufacturing expertise in the general marketplace. In addition, the Company considers whether the collaborator can use the license or other deliverables for their intended purpose without the receipt of the remaining elements, and whether the value of the deliverable is dependent on the undelivered items and whether there are other vendors that can provide the undelivered items.

The consideration received is allocated among the separate units of accounting using the relative selling price method, and the applicable revenue recognition criteria are applied to each of the separate units.

The Company determines the estimated selling price for deliverables using vendor-specific objective evidence ("VSOE") of selling price, if available, third-party evidence ("TPE") of selling price if VSOE is not available, or best estimate of selling price ("BESP") if neither VSOE nor TPE is available. Determining the BESP for a deliverable requires significant judgment. The Company uses BESP to estimate the selling price for licenses to the Company's proprietary technology, since the Company often does not have VSOE or TPE of selling price for these deliverables. In those circumstances where the Company utilizes BESP to determine the estimated selling price of a license to the Company's proprietary technology, the Company considers market conditions as well as entity-specific factors, including those factors contemplated in negotiating the agreements as well as internally developed models that include assumptions related to the market opportunity, estimated development costs, probability of success and the time needed to commercialize a product candidate pursuant to the license. In validating the Company's BESP, the Company evaluates whether changes in the key assumptions used to determine the BESP will have a significant effect on the allocation of arrangement consideration between multiple deliverables.

At December 31, 2013, the Company has one collaboration agreement with AstraZeneca that is being accounted for under ASU 2009-13.

Up-Front License Fees

When management believes the license to its intellectual property has stand-alone value, the Company generally recognizes revenue attributed to the license upon delivery. When management believes the license to its intellectual property does not have stand-alone value from the other deliverables to be provided in the arrangement, it is combined with other deliverables and the revenue of the combined unit of accounting is recorded based on the method appropriate for the last delivered item.

Milestones

At the inception of each arrangement that includes pre-commercial milestone payments, the Company evaluates whether each pre-commercial milestone is substantive, in accordance with ASU No. 2010-17, Revenue Recognition—Milestone Method ("ASU 2010-17"), adopted on January 1, 2011. This evaluation includes an assessment of whether (a) the consideration is commensurate with either (1) the entity's performance to achieve the milestone, or (2) the enhancement of the value of the delivered item(s) as a result of a specific outcome resulting from the entity's performance to achieve the milestone, (b) the consideration relates solely to past performance and (c) the consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. The Company evaluates factors such as the scientific, clinical, regulatory, commercial and other risks that must be overcome to achieve the respective milestone, the level of effort and investment required and whether the milestone consideration is reasonable relative to all deliverables and payment terms in the arrangement in making this assessment. At December 31, 2013, the Company had no pre-commercial milestones that were deemed substantive. If a substantive pre-commercial milestone is achieved and collection of the related receivable is reasonably assured, the Company recognizes revenue related to the milestone in its entirety in the period in which the milestone is achieved. If the Company were to achieve milestones that are considered substantive under any of the Company's collaborations, the Company may experience significant fluctuations in collaborative arrangements revenue from quarter to quarter and year to year depending on the timing of achieving such substantive milestones. In those circumstances where a pre-commercial milestone is not substantive, the Company recognizes as revenue on the date the milestone is achieved an amount equal to the applicable percentage of the performance period that had elapsed as of the date the milestone was achieved, with the balance being deferred and recognized over the remaining period of performance. Pre-commercial milestone payments received prior to the adoption of ASU 2010-17 continue to be recognized over the remaining period of performance.

Commercial milestones are accounted for as royalties and are recorded as revenue upon achievement of the milestone, assuming all other revenue recognition criteria are met.

Net Profit or Net Loss Sharing

In accordance with ASC 808 Topic, Collaborative Arrangements, and ASC 605-45, Principal Agent Considerations, the Company considers the nature and contractual terms of the arrangement and the nature of the Company's business operations to determine the classification of the transactions under the Company's collaboration agreements. The Company records revenue transactions gross in the consolidated statements of operations if it is deemed the principal in the transaction, which includes being the primary obligor and having the risks and rewards of ownership.

The Company recognizes its share of the pre-tax commercial net profit or net loss generated from the sales of LINZESS in the U.S. in the period the product sales are reported by Forest and related cost of goods sold and selling, general and administrative expenses are incurred by the Company and its collaboration partner. These amounts are partially determined based on amounts provided by Forest and involve the use of estimates and judgments, such as product sales allowances and accruals related to prompt payment discounts, chargebacks, governmental and contractual rebates, wholesaler fees, product returns, and co-payment assistance costs, which could be adjusted based on actual results in the future. The Company is highly dependent on Forest for timely and accurate information regarding any net revenues realized from sales of LINZESS and the costs incurred in selling it, in order to accurately report its results of operations. For the periods covered in the consolidated financial statements presented, there have been no material changes to prior period estimates of revenues, cost of goods sold or selling, general and administrative expenses associated with the sales of LINZESS in the U.S. However, if the Company does not receive timely and accurate information or incorrectly estimates activity levels associated with the collaboration at a given point in time, the Company could be required to record adjustments in future periods.

The Company records its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis and presents the settlement payments to and from Forest as collaboration expense or collaborative arrangements revenue, as applicable, as the Company is not the primary obligor and does not have the risks and rewards of ownership in the collaboration agreement with Forest. The Company and Forest settle the cost sharing quarterly, such that the Company's statement of operations reflects 50% of the pre-tax net profit or loss generated from sales of LINZESS in the U.S. Prior to the fourth quarter of 2012, selling, general and administrative cost-sharing payments were presented within selling, general and administrative expenses. The cost-sharing payments to Forest for the nine months ended September 30, 2012 were reclassified to conform to the current period's presentation. Prior to 2012, such selling, general and administrative cost-sharing payments were presented within selling, general and administrative expenses and were not material to the consolidated financial statements.

Royalties on Product Sales

The Company receives or expects to receive in the future royalty revenues under certain of the Company's license or collaboration agreements. If the Company does not have any future performance obligations under these license or collaborations agreements, the Company records these revenues as earned. To the extent the Company does not have access to the royalty reports from the Company's partners or the ability to accurately estimate the royalty revenue in the period earned, the Company records such royalty revenues one quarter in arrears.

Other

The Company produces finished drug product, API and development materials for certain of its collaborators. The Company recognizes revenue on finished drug product, API and development materials when the material has passed all quality testing required for collaborator acceptance, delivery has occurred, title and risk of loss have transferred to the collaborator, the price is fixed or determinable, and collection is reasonably assured. As it relates to development materials and API produced for Almirall and Astellas, the Company is reimbursed at a contracted rate. Such reimbursements are considered as part of revenue generated pursuant to the Almirall and Astellas license agreements and are presented as collaborative arrangements revenue. Any finished drug product, API and development materials currently produced for Forest or AstraZeneca are recognized in accordance with the cost-sharing provisions of the Forest and AstraZeneca collaboration agreements, respectively.

Cost of Revenue

Cost of revenue is recognized upon shipment of linaclotide API to certain of the Company's collaboration partners and consists of the costs of producing such API. The costs of API were primarily recorded as research and development expenses in the periods prior to July 1, 2012. In the third quarter of 2012, the Company began capitalizing inventory costs for linaclotide API manufactured in preparation for its launch of linaclotide in the U.S. and Europe based on its evaluation of, among other factors, the status of the LINZESS NDAs in the U.S., the Committee for Medicinal Products for Human Use ("CHMP") positive recommendation to grant marketing approval for CONSTELLA in Europe, and the ability of the Company's third-party suppliers to successfully manufacture commercial quantities of linaclotide API, which provided the Company with reasonable assurance that the net realizable value of the inventory would be recoverable. As of December 31, 2012, the previously expensed commercial API inventory was substantially utilized.

Research and Development Costs

The Company expenses research and development costs to operations as incurred. The Company defers and capitalizes nonrefundable advance payments made by the Company for research and development activities until the related goods are received or the related services are performed.

Research and development expenses are comprised of costs incurred in performing research and development activities, including salary, benefits and other employee-related expenses; share-based compensation expense; laboratory supplies and other direct expenses; facilities expenses; overhead expenses; third-party contractual costs relating to nonclinical studies and clinical trial activities and related contract manufacturing expenses, development of manufacturing processes and regulatory registration of third-party manufacturing facilities; costs associated with linaclotide API prior to the Company concluding that regulatory approval is probable and that its net realizable value is recoverable; licensing fees for our product candidates; and other outside expenses.

The Company has entered into collaboration agreements with Forest and AstraZeneca pursuant to which it shares research and development expenses with the collaborators. The Company records expenses incurred under the collaboration arrangements for such work as research and development expense. Because the collaboration arrangements are cost-sharing arrangements, the Company concluded that when there is a period during the collaboration arrangements during which the Company receives payments from Forest or AstraZeneca, the Company records the payments by Forest or AstraZeneca for their share of the development effort as a reduction of research and development expense. Payments to Forest or AstraZeneca are recorded as incremental research and development expense.

Selling, General and Administrative Expenses

The Company expenses selling, general and administrative costs to operations as incurred. Selling, general and administrative expense consists primarily of compensation, benefits and other employee-related expenses for personnel in our administrative, finance, legal, information technology, business development, commercial, sales, marketing, communications and human resource functions. Other costs include the legal costs of pursuing patent protection of the Company's intellectual property, general and administrative related facility costs and professional fees for accounting and legal services.

Under the Forest and AstraZeneca collaboration agreements, the Company is reimbursed for certain selling, general and administrative expenses and it nets these reimbursements against selling, general and administrative expenses as incurred. Payments to Forest or AstraZeneca are recorded as incremental selling, general and administrative expense.

Beginning in the fourth quarter of 2012, the Company includes Forest's selling, general and administrative cost-sharing payments in the calculation of the net profits and net losses from the sale of LINZESS in the U.S. and presents the net payment to or from Forest as collaboration expense or collaborative arrangements revenue, as applicable. The selling, general and administrative cost-sharing payments to Forest for the nine months ended September 30, 2012 were reclassified to conform to the current presentation. Prior to 2012, such Forest-related selling, general and administrative cost-sharing payments were presented within selling, general and administrative expenses and were not material to the consolidated financial statements.

Share-Based Compensation

The Company's stock-based compensation programs grant awards which have included stock awards, restricted stock, and stock options. Share-based compensation is recognized as an expense in the financial statements based on the grant date fair value over the requisite service period. For awards that vest based on service conditions, the Company uses the straight-line method to allocate compensation expense to reporting periods. The grant date fair value of options granted is calculated using the Black-Scholes option-pricing model, which requires the use of subjective assumptions including volatility and expected term, among others.

The Company records the expense for stock option grants subject to performance-based milestone vesting using the accelerated attribution method over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates when the achievement of a performance-based milestone is probable based on the relative satisfaction of the performance conditions as of the reporting date.

The Company records the expense of services rendered by non-employees based on the estimated fair value of the stock option using the Black-Scholes option-pricing model. The fair value of unvested non-employee awards is remeasured at each reporting period and expensed over the vesting term of the underlying stock options.

Patent Costs

The Company incurred and recorded as operating expense legal and other fees related to patents of approximately $3.2 million, approximately $3.5 million, and approximately $2.2 million for the years ended December 31, 2013, 2012 and 2011, respectively. These costs were charged to selling, general and administrative expenses as incurred.

Net Income (Loss) Per Share

The Company calculates basic net income (loss) per common share and diluted net loss per common share by dividing the net income (loss) by the weighted average number of common shares outstanding during the period. Diluted net income per common share is computed by dividing net income by the diluted number of shares outstanding during the period. Except where the result would be antidilutive to net income, diluted net income per share is computed assuming the exercise of common stock options and the vesting of restricted stock (using the treasury stock method), as well as their related income tax effects. The Company allocates undistributed earnings between the classes on a one-to-one basis when computing net income (loss) per share. As a result, basic and diluted net income (loss) per Class A and Class B shares are equivalent.

Property and Equipment

Property and equipment, including leasehold improvements, are recorded at cost, and are depreciated when placed into service using the straight-line method based on their estimated useful lives as follows:

Asset Description

Estimated Useful Life

(In Years)

Manufacturing equipment

10

Laboratory equipment

5

Computer and office equipment

3

Furniture and fixtures

7

Software

3

Included in property and equipment are certain costs of software obtained for internal use. Costs incurred during the preliminary project stage are expensed as incurred, while costs incurred during the application development stage are capitalized and amortized over the estimated useful life of the software. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditures will result in additional functionality. Maintenance and training costs related to software obtained for internal use are expensed as incurred.

Leasehold improvements are amortized over the shorter of the estimated useful life of the asset or the lease term. Capital lease assets are amortized over the lease term. However, if ownership was transferred by the end of the capital lease, or there was a bargain purchase option, such capital lease assets would be amortized over the useful life that would be assigned if such assets were owned.

Costs for capital assets not yet placed into service have been capitalized as construction in progress, and will be depreciated in accordance with the above guidelines once placed into service. Maintenance and repair costs are expensed as incurred.

Income Taxes

The Company provides for income taxes under the liability method. Deferred tax assets and liabilities are determined based on differences between financial reporting and tax bases of assets and liabilities and are measured using the enacted tax rates in effect when the differences are expected to reverse. Deferred tax assets are reduced by a valuation allowance to reflect the uncertainty associated with their ultimate realization.

The Company accounts for uncertain tax positions recognized in the consolidated financial statements by prescribing a more-likely-than-not threshold for financial statement recognition and measurement of a tax position taken or expected to be taken in a tax return.

Impairment of Long-Lived Assets

The Company regularly reviews the carrying amount of its long-lived assets to determine whether indicators of impairment may exist, which warrant adjustments to carrying values or estimated useful lives. If indications of impairment exist, projected future undiscounted cash flows associated with the asset are compared to the carrying amount to determine whether the asset's value is recoverable. If the carrying value of the asset exceeds such projected undiscounted cash flows, the asset will be written down to its estimated fair value. There were no significant impairments of long-lived assets for the years ended December 31, 2013, 2012 or 2011.

Comprehensive Income (Loss)

Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions, and other events and circumstances from non-owner sources and currently consists of net loss and changes in unrealized gains and losses on available-for-sale securities.

Segment Information

Operating segments are components of an enterprise for which separate financial information is available and is evaluated regularly by the Company's chief operating decision-maker in deciding how to allocate resources and in assessing performance. The Company currently operates in one reportable business segment—human therapeutics.

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board or other standard setting bodies that are adopted by the Company as of the specified effective date. The Company did not adopt any new accounting pronouncements during the year ended December 31, 2013 that had a material effect on its consolidated financial statements.

Net_Loss_Per_Share

Net Loss Per Share	12 Months Ended
	Dec. 31, 2013
Net Loss Per Share	'
Net Loss Per Share	'
	3. Net Loss Per Share
	The following table sets forth the computation of basic and diluted net loss per share (in thousands, except per share amounts):
		Years Ended December 31,
		2013			2012			2011
	Numerator:
	Net loss	$	(272,812	)	$	(72,624	)	$	(64,852	)
	Denominator:
	Weighted average number of common shares used in net loss per share—basic and diluted		115,852			106,403			99,875
	Net loss per share—basic and diluted	$	(2.35	)	$	(0.68	)	$	(0.65	)
	The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding as they would be anti-dilutive (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Options to purchase common stock		20,928			19,540			16,425
	Shares subject to repurchase		—			80			160
			20,928			19,620			16,585
	The number of shares issuable under the Company's employee stock purchase plan that were excluded from the calculation of diluted weighted average shares outstanding because their effects would be anti-dilutive was insignificant.

Collaboration_and_License_Agre

Collaboration and License Agreements	12 Months Ended
	Dec. 31, 2013
Collaboration and License Agreements	'
Collaboration and License Agreements	'
	4. Collaboration and License Agreements
	Forest Laboratories, Inc.
	In September 2007, the Company entered into a collaboration agreement with Forest to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in North America. Under the terms of this collaboration agreement, the Company shares equally with Forest all development costs as well as future net profits or losses from the development and sale of linaclotide in the U.S. The Company will also receive royalties in the mid-teens percent based on net sales in Canada and Mexico. Forest is solely responsible for the further development, regulatory approval and commercialization of linaclotide in those countries and funding any costs. In September 2012, Forest sublicensed its commercialization rights in Mexico to Almirall. Forest made non-refundable, up-front payments totaling $70.0 million to the Company in order to obtain rights to linaclotide in North America. Because the license to jointly develop and commercialize linaclotide did not have a standalone value without research and development activities provided by the Company, the Company recorded the up-front license fee as collaborative arrangements revenue on a straight-line basis through September 30, 2012, the period over which linaclotide was jointly developed under the collaboration. The collaboration agreement also includes contingent milestone payments, as well as a contingent equity investment, based on the achievement of specific development and commercial milestones. At December 31, 2013, $205.0 million in license fees and development milestone payments had been received by the Company, as well as a $25.0 million equity investment in the Company's capital stock. The Company can also achieve up to $100.0 million in a sales related milestone if certain conditions are met.
	The collaboration agreement included a contingent equity investment, in the form of a forward purchase contract, which required Forest to purchase shares of the Company's convertible preferred stock upon achievement of a specific development milestone. At the inception of the arrangement, the Company valued the contingent equity investment and recorded an approximately $9.0 million asset and incremental deferred revenue. The $9.0 million of incremental deferred revenue was recognized as collaborative arrangements revenue on a straight-line basis over the period of the Company's continuing involvement through September 30, 2012. In July 2009, the Company achieved the development milestone triggering the equity investment and reclassified the forward purchase contract as a reduction to convertible preferred stock. On September 1, 2009, the Company issued 2,083,333 shares of convertible preferred stock to Forest (Note 16).
	The Company achieved all six development milestones under this agreement. In September 2008 and July 2009, the Company achieved development milestones which triggered $10.0 million and $20.0 million milestone payments, respectively. These development milestones were recognized as collaborative arrangements revenue through September 2012. In October 2011, the Company achieved two development milestones upon the FDA's acceptance of the linaclotide New Drug Applications ("NDA") for both IBS-C and CIC in adults and received milestone payments totaling $20.0 million from Forest. In August 2012, the Company achieved two additional development milestones upon the FDA's approval of the linaclotide NDAs for both IBS-C and CIC in adults and received milestone payments totaling $85.0 million from Forest in September 2012, accordingly. In accordance with ASU 2010-17, these four development milestones were recognized as collaborative arrangements revenue in their entirety upon achievement. The remaining milestone payment that could be received from Forest upon the achievement of sales targets will be recognized as collaborative arrangements revenue as earned.
	As a result of the research and development cost-sharing provisions of the collaboration, the Company recognized approximately $2.2 million and approximately $2.1 million in incremental research and development costs during the years ended December 31, 2013 and 2012, respectively, and offset approximately $7.9 million against research and development costs in the year ended December 31, 2011, to reflect its obligation under the collaboration to bear half of the development costs incurred by both parties.
	The Company receives 50% of the net profits and bears 50% of the net losses from the commercial sale of LINZESS in the U.S., provided, however, that if either party provides fewer calls on physicians in a particular year than it is contractually required to provide, such party's share of the net profits will be reduced as stipulated by the collaboration agreement. Net profits or net losses consist of net sales to third-party customers and sublicense income in the U.S. less cost of goods sold as well as selling, general and administrative expenses. Net sales are calculated and recorded by Forest and may include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions. The Company and Forest began commercializing LINZESS in December 2012.
	The Company recognized collaborative arrangements revenue from the Forest collaboration agreement totaling approximately $2.9 million, approximately $100.4 million and approximately $41.8 million during the years ended December 31, 2013, 2012 and 2011, respectively. The collaborative arrangements revenue recognized in the year ended December 31, 2013 represents the Company's share of the net profits and net losses on the sale of LINZESS in the U.S. The collaborative arrangements revenue recognized in the years ended December 2012 and 2011 related to the substantive pre-commercial milestones earned and the amortization of deferred revenue.
	The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the years ended December 31, 2013 and 2012 (in thousands):
		Year Ended
		December 31,
		2013			2012
	Collaborative arrangements revenue(1)	$	2,914		$	—
	Collaboration expense		(42,074	)		(16,030	)
	Selling, general and administrative costs incurred by the Company(1)		(33,839	)		(5,092	)
	The Company's share of net loss	$	(72,999	)	$	(21,122	)
	-1
	Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Forest.
	Prior to 2012, selling, general and administrative cost-sharing payments presented within selling, general and administrative expenses were not material.
	Almirall, S.A.
	In April 2009, the Company entered into a license agreement with Almirall to develop and commercialize linaclotide in Europe (including the Commonwealth of Independent States and Turkey) for the treatment of IBS-C, CIC and other GI conditions. Under the terms of the license agreement, Almirall is responsible for the expenses associated with the development and commercialization of linaclotide in the European territory and the Company was required to participate on a joint development committee over linaclotide's development period.
	In May 2009, the Company received an approximately $38.0 million payment from Almirall representing a $40.0 million non-refundable up-front payment net of foreign withholding taxes. The Company elected to record the non-refundable up-front payment net of taxes withheld. The Company recognized the up-front license fee as collaborative arrangements revenue on a straight-line basis through September 30, 2012, the period over which linaclotide was developed under the license agreement.
	The license agreement also included a $15.0 million contingent equity investment, in the form of a forward purchase contract, which required Almirall to purchase shares of the Company's convertible preferred stock upon achievement of a specific development milestone. At the inception of the arrangement, the Company valued the contingent equity investment and recorded an approximately $6.0 million asset and incremental deferred revenue. The $6.0 million of incremental deferred revenue was recognized as collaborative arrangements revenue through September 2012. In November 2009, the Company achieved the development milestone triggering the equity investment and reclassified the forward purchase contract as a reduction to convertible preferred stock. On November 13, 2009, the Company received $15.0 million from Almirall for the purchase of 681,819 shares of convertible preferred stock (Note 16).
	The original license agreement also included contingent milestone payments that could total up to $40.0 million upon achievement of specific development and commercial launch milestones. In November 2010, the Company achieved a development milestone, which resulted in a $19.0 million payment, representing a $20.0 million milestone, net of foreign withholding taxes. This development milestone was recognized as collaborative arrangements revenue through September 2012. Commercial milestone payments under the original license agreement consisted of $4.0 million due upon the first commercial launch in each of the five major E.U. countries set forth in the agreement.
	In June 2013, the Company and Almirall amended the original license agreement. Pursuant to the terms of the amendment, (i) the commercial launch milestones were reduced to $17.0 million; (ii) new sales-based milestone payments were added to the agreement; and (iii) the escalating royalties based on sales of linaclotide were modified such that they begin in the low-twenties percent and escalate to the mid-forties percent through April 2017, and thereafter begin in the mid-twenties percent and escalate to the mid-forties percent at lower sales thresholds. In each case, these royalty payments are reduced by the transfer price paid for the API included in the product actually sold in the Almirall territory and other contractual deductions. The Company concluded that the amendment was not a material modification of the license agreement. The commercial launch and sales-based milestones are recognized as revenue as earned. The Company records royalties on sales of CONSTELLA one quarter in arrears as it does not have access to the royalty reports from Almirall or the ability to estimate the royalty revenue in the period earned.
	During the second quarter of 2013, the Company achieved two milestones under the amended Almirall license agreement, which resulted in payments of approximately $1.9 million from Almirall to the Company related to the commercial launches in two of the five major E.U. countries, the United Kingdom and Germany. The approximately $1.9 million payment represented the two $1.0 million milestones, net of foreign tax withholdings.
	The Company recognized approximately $13.1 million, approximately $21.2 million and approximately $20.6 million in total collaborative arrangements revenue from the Almirall license agreement during the years ended December 31, 2013, 2012 and 2011, respectively, including approximately $11.1 million, approximately $3.5 million and approximately $0.5 million, respectively, in revenue from the sale of API to Almirall as well as approximately $0.2 million in royalty revenue and approximately $1.9 million in commercial launch milestones in the year ended December 31, 2013.
	Astellas Pharma Inc.
	In November 2009, the Company entered into a license agreement with Astellas to develop and commercialize linaclotide for the treatment of IBS-C, CIC and other GI conditions in Japan, South Korea, Taiwan, Thailand, the Philippines and Indonesia. As a result of an amendment executed in March 2013, the Company regained rights to linaclotide in South Korea, Taiwan, Thailand, the Philippines and Indonesia. The Company concluded that the amendment was not a material modification of the license agreement. Astellas continues to be responsible for all activities relating to development, regulatory approval and commercialization in Japan as well as funding any costs and the Company is required to participate on a joint development committee over linaclotide's development period.
	In 2009, Astellas paid the Company a non-refundable, up-front licensing fee of $30.0 million, which is being recognized as collaborative arrangements revenue on a straight-line basis over the Company's estimate of the period over which linaclotide will be developed under the license agreement. In March 2013, the Company revised its estimate of the development period from 115 months to 85 months based on the Company's assessment of regulatory approval timelines for Japan. This resulted in the recognition of an additional approximately $1.5 million of revenue in the year ended December 31, 2013.
	The agreement also includes additional development milestone payments that could total up to $45.0 million. These milestone payments, none of which the Company considers substantive, consist of $15.0 million upon initiation of a Phase III study for linaclotide in Japan, $15.0 million upon filing of the Japanese equivalent of an NDA with the relevant regulatory authority in Japan, and $15.0 million upon approval of such equivalent by the relevant regulatory authority. In addition, the Company will receive royalties which escalate based on sales volume, beginning in the low-twenties percent, less the transfer price paid for the API included in the product actually sold and other contractual deductions.
	At December 31, 2013, approximately $16.5 million of the up-front license fee remains deferred. During the years ended December 31, 2013, 2012 and 2011, the Company recognized approximately $5.8 million, approximately $3.9 million and approximately $3.5 million, respectively, in revenue from the Astellas license agreement, including approximately $1.2 million, approximately $0.8 million, and approximately $0.4 million, respectively, from the sale of API to Astellas.
	AstraZeneca AB
	In October 2012, the Company entered into a collaboration agreement with AstraZeneca (the "AstraZeneca Collaboration Agreement") to co-develop and co-commercialize linaclotide in China, Hong Kong and Macau (the "License Territory"). The collaboration provides AstraZeneca with an exclusive nontransferable license to exploit the underlying technology in the License Territory. The parties will share responsibility for continued development and commercialization of linaclotide under a joint development plan and a joint commercialization plan, respectively, with AstraZeneca having primary responsibility for the local operational execution.
	The parties agreed to an Initial Development Plan ("IDP") which includes the planned development of linaclotide in China, including the lead responsibility for each activity and the related internal and external costs. The IDP indicates that AstraZeneca is responsible for a multinational Phase III clinical trial, the Company is responsible for nonclinical development and supplying clinical trial material and both parties are responsible for the regulatory submission process. The IDP indicates that the party specifically designated as being responsible for a particular development activity under the IDP shall implement and conduct such activities. The activities are governed by a Joint Development Committee ("JDC"), with equal representation from each party. The JDC is responsible for approving, by unanimous consent, the joint development plan and development budget, as well as approving protocols for clinical studies, reviewing and commenting on regulatory submissions, and providing an exchange of data information.
	The AstraZeneca Collaboration Agreement will continue until there is no longer a development plan or commercialization plan in place, however, it can be terminated by AstraZeneca at any time upon 180 days' prior written notice. Under certain circumstances, either party may terminate the AstraZeneca Collaboration Agreement in the event of bankruptcy or an uncured material breach of the other party. Upon certain change in control scenarios of AstraZeneca, the Company may elect to terminate the AstraZeneca Collaboration Agreement and may re-acquire its product rights in a lump sum payment equal to the fair market value of such product rights.
	In connection with the AstraZeneca Collaboration Agreement, the Company and AstraZeneca also executed a co-promotion agreement (the "Co-Promotion Agreement"), pursuant to which the Company will utilize its existing sales force to co-promote NEXIUM® (esomeprazole magnesium), one of AstraZeneca's products, in the U.S. The Co-Promotion Agreement expires upon the earlier of May 27, 2014 or the date on which a generic version of AstraZeneca's product is first sold in the U.S. The Company may terminate the Co-Promotion Agreement on or after December 31, 2013 upon written notice to AstraZeneca.
	There are no refund provisions in the AstraZeneca Collaboration Agreement and the Co-Promotion Agreement (together, the "AstraZeneca Agreements").
	Under the terms of the AstraZeneca Collaboration Agreement, the Company received a $25.0 million non-refundable upfront payment upon execution. The Company is also eligible for $125.0 million in additional commercial milestone payments contingent on the achievement of certain sales targets. The parties will also share in the net profits and losses associated with the development and commercialization of linaclotide in the License Territory, with AstraZeneca receiving 55% of the net profits or incurring 55% of the net losses until a certain specified commercial milestone is achieved, at which time profits and losses will be shared equally thereafter.
	Activities under the AstraZeneca Agreements were evaluated in accordance with ASC 605-25 to determine if they represented a multiple element revenue arrangement. The Company identified the following deliverables in the AstraZeneca Agreements:
	•
	an exclusive license to develop and commercialize linaclotide in the License Territory (the "License Deliverable"),
	•
	research, development and regulatory services pursuant to the IDP (the "R&D Services"),
	•
	JDC services,
	•
	obligation to supply clinical trial material, and
	•
	co-promotion services for AstraZeneca's product (the "Co-Promotion Deliverable").
	The License Deliverable is nontransferable and has certain sublicense restrictions. The Company determined that the License Deliverable had standalone value as a result of AstraZeneca's internal product development and commercialization capabilities, which would enable it to use the License Deliverable for its intended purposes without the involvement of the Company. The remaining deliverables were deemed to have standalone value based on their nature and all deliverables met the criteria to be accounted for as separate units of accounting under ASC 605-25. Factors considered in this determination included, among other things, whether any other vendors sell the items separately and if the customer could use the delivered item for its intended purpose without the receipt of the remaining deliverables.
	The Company identified the supply of linaclotide drug product for commercial requirements and commercialization services as contingent deliverables because these services are contingent upon the receipt of regulatory approval to commercialize linaclotide in the License Territory, and there were no binding commitments or firm purchase orders pending for commercial supply. As these deliverables are contingent, and are not at an incremental discount, they are not evaluated as deliverables at the inception of the arrangement. These contingent deliverables will be evaluated and accounted for separately as each related contingency is resolved. As of December 31, 2013, no contingent deliverables were provided by the Company under the AstraZeneca Agreements.
	The total amount of the non-contingent consideration allocable to the AstraZeneca Agreements of approximately $26.9 million ("Arrangement Consideration") includes the $25.0 million non-refundable upfront payment and 55% of the costs for clinical trial material supply services and research, development and regulatory activities allocated to the Company in the IDP, or approximately $1.9 million. The Company allocated the Arrangement Consideration of approximately $26.9 million to the non-contingent deliverables based on management's BESP of each deliverable using the relative selling price method as the Company did not have VSOE or TPE of selling price for such deliverables. The Company estimated the BESP for the License Deliverable using a multi-period excess-earnings method under the income approach which utilized cash flow projections, the key assumptions of which included the following market conditions and entity-specific factors: (a) the specific rights provided under the license to develop and commercialize linaclotide; (b) the potential indications for linaclotide pursuant to the license; (c) the likelihood linaclotide will be developed for more than one indication; (c) the stage of development of linaclotide for IBS-C and CIC and the projected timeline for regulatory approval; (d) the development risk by indication; (f) the market size by indication; (g) the expected product life of linaclotide assuming commercialization; (h) the competitive environment, and (i) the estimated development and commercialization costs of linaclotide in the License Territory. The Company utilized a discount rate of 11.5% in its analysis, representing the weighted average cost of capital derived from returns on equity for comparable companies. The Company determined its BESP for the remaining deliverables based on the nature of the services to be performed and estimates of the associated effort and cost of the services adjusted for a reasonable profit margin such that they represented estimated market rates for similar services sold on a standalone basis.
	The Company concluded that a change in key assumptions used to determine BESP for each deliverable would not have a significant effect on the allocation of the Arrangement Consideration, as the estimated selling price of the License Deliverable significantly exceeds the other deliverables.
	Of the approximately $26.9 million Arrangement Consideration, approximately $24.7 million was allocated to the License Deliverable, approximately $0.3 million to the R&D Services, approximately $28,000 to the JDC services, approximately $0.1 million to the clinical trial material supply services, and approximately $1.8 million to the Co-Promotion Deliverable in the relative selling price model. The Company recognized all $24.7 million allocated to the License Deliverable as revenue upon the execution of the AstraZeneca Agreements as the associated unit of accounting had been delivered and there is no general right of return. At inception, the remaining approximately $0.3 million of the Arrangement Consideration received and allocated to the remaining deliverables based on their relative selling prices, was deferred.
	Because the Company shares development costs with AstraZeneca, payments from AstraZeneca with respect to both research and development and selling, general and administrative costs incurred by the Company prior to the commercialization of linaclotide in the License Territory are recorded as a reduction to expense, in accordance with the Company's policy, which is consistent with the nature of the cost reimbursement. Development costs incurred by the Company that pertain to the IDP are recorded as research and development expense as incurred. Payments to AstraZeneca are recorded as incremental research and development expense.
	The Company will perform the R&D Services, JDC services and supply clinical trial materials during the estimated development period of approximately 44 months. All Arrangement Consideration allocated to such services is being recognized as a reduction of research and development costs, using the proportional performance method, by which the amounts are recognized in proportion to the costs incurred. As a result of the cost-sharing arrangements under the collaboration, the Company recognized approximately $1.9 million in incremental research and development costs during the year ended December 31, 2013. Research and development costs incurred during the year ended December 31, 2012 were not significant.
	The amount allocated to the Co-Promotion Deliverable is being recognized as collaborative arrangements revenue using the proportional performance method, which approximates recognition on a straight-line basis beginning on the date that the Company began to co-promote AstraZeneca's product, through December 31, 2013 (the earliest cancellation date). Through December 31, 2013, the Company earned all consideration allocated to the Co-Promotion Deliverable but recognized approximately $1.0 million as collaborative arrangement revenue. The revenue recognized in the statement of operations was limited to the non-contingent consideration at December 31, 2013 in accordance with ASC 605-25.
	The Company reassesses the periods of performance for each deliverable at the end of each reporting period.
	Milestone payments received from AstraZeneca upon the achievement of sales targets will be recognized as earned.
	Other Collaboration and License Agreements
	The Company has other collaboration and license agreements that are not individually significant to its business. In connection with entering into these agreements, the Company made aggregate up-front payments of approximately $5.8 million, which were expensed as research and development expense. Pursuant to the terms of certain of those agreements, the Company may be required to pay $99.5 million for development milestones, of which $1.0 million had been paid, and $265.5 million for regulatory milestones, none of which had been paid, in each case as of December 31, 2013. In addition, pursuant to the terms of another agreement, the contingent milestones could total up to $114.5 million per product to one of the Company's collaboration partners, including $21.5 million for development milestones, $58.0 million for regulatory milestones and $35.0 million for sales-based milestones. Further, under such agreements, the Company is also required to fund certain research activities and, if any product related to these collaborations is approved for marketing, to pay significant royalties on future sales. During the years ended December 31, 2013, 2012 and 2011, the Company incurred approximately $3.6 million, approximately $8.2 million and approximately $6.0 million, respectively, in research and development expense associated with the Company's other collaboration and license agreements.

Fair_Value_of_Financial_Instru

Fair Value of Financial Instruments	12 Months Ended
	Dec. 31, 2013
Fair Value of Financial Instruments	'
Fair Value of Financial Instruments	'
	5. Fair Value of Financial Instruments
	The tables below present information about the Company's assets that are measured at fair value on a recurring basis as of December 31, 2013 and 2012 and indicate the fair value hierarchy of the valuation techniques the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize observable inputs such as quoted prices in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are either directly or indirectly observable, such as quoted prices, interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the Company to develop its own assumptions for the asset or liability.
	The Company's investment portfolio includes many fixed income securities that do not always trade on a daily basis. As a result, the pricing services used by the Company apply other available information as applicable through processes such as benchmark yields, benchmarking of like securities, sector groupings and matrix pricing to prepare valuations. In addition, model processes were used to assess interest rate impact and develop prepayment scenarios. These models take into consideration relevant credit information, perceived market movements, sector news and economic events. The inputs into these models may include benchmark yields, reported trades, broker-dealer quotes, issuer spreads and other relevant data.
	The following tables present the assets the Company has measured at fair value on a recurring basis (in thousands):
				Fair Value Measurements at Reporting Date Using
	Description	December 31,		Quoted Prices in		Significant Other		Significant
		2013		Active Markets for		Observable		Unobservable
				Identical Assets		Inputs		Inputs
				(Level 1)		(Level 2)		(Level 3)
	Cash and cash equivalents:
	Money market funds	$	59,747	$	59,747	$	—	$	—
	U.S. government-sponsored securities		7,505		—		7,505		—
	Available-for-sale securities:
	U.S. Treasury securities		7,253		7,253		—		—
	U.S. government-sponsored securities		114,859		—		114,859		—
	Total	$	189,364	$	67,000	$	122,364	$	—
				Fair Value Measurements at Reporting Date Using
	Description	December 31,		Quoted Prices in		Significant Other		Significant
		2012		Active Markets for		Observable		Unobservable
				Identical Assets		Inputs		Inputs
				(Level 1)		(Level 2)		(Level 3)
	Cash and cash equivalents:
	Money market funds	$	111,368	$	111,368	$	—	$	—
	U.S. government-sponsored securities		2,500		—		2,500		—
	Available-for-sale securities:
	U.S. Treasury securities		15,052		15,052		—		—
	U.S. government-sponsored securities		16,476		—		16,476		—
	Total	$	145,396	$	126,420	$	18,976	$	—
	There were no transfers between Level 1 and Level 2 of the fair value hierarchy during the years ended December 31, 2013 or 2012.
	Cash equivalents, accounts receivable, including related party accounts receivable, prepaid expenses and other current assets, accounts payable, accrued expenses and the current portion of capital lease obligations at December 31, 2013 and 2012 are carried at amounts that approximate fair value due to their short-term maturities.
	The non-current portion of the capital lease obligations at December 31, 2013 and 2012 approximates fair value as it bears interest at a rate approximating a market interest rate.

AvailableforSale_Securities

Available-for-Sale Securities	12 Months Ended
	Dec. 31, 2013
Available-for-Sale Securities	'
Available-for-Sale Securities	'
	6. Available-for-Sale Securities
	The following tables summarize the available-for-sale securities held at December 31, 2013 and 2012 (in thousands):
		Amortized Cost		Gross		Gross			Fair Value
				Unrealized		Unrealized
				Gains		Losses
	December 31, 2013:
	U.S. government-sponsored securities	$	114,857	$	6	$	(4	)	$	114,859
	U.S. Treasury securities		7,253		—		—			7,253
	Total	$	122,110	$	6	$	(4	)	$	122,112
		Amortized Cost		Gross		Gross			Fair Value
				Unrealized		Unrealized
				Gains		Losses
	December 31, 2012:
	U.S. government-sponsored securities	$	16,472	$	5	$	(1	)	$	16,476
	U.S. Treasury securities		15,051		1		—			15,052
	Total	$	31,523	$	6	$	(1	)	$	31,528
	The contractual maturities of all securities held at December 31, 2013 are one year or less. There were 12 and 3 investments classified as available-for-sale securities in an unrealized loss position at December 31, 2013 and 2012, respectively, none of which had been in an unrealized loss position for more than twelve months. The aggregate fair value of these securities at December 31, 2013 and 2012 was approximately $38.7 million and approximately $3.0 million, respectively. The Company reviews its investments for other-than-temporary impairment whenever the fair value of an investment is less than amortized cost and evidence indicates that an investment's carrying amount is not recoverable within a reasonable period of time. To determine whether impairment is other-than-temporary, the Company considers whether it has the ability and intent to hold the investment until a market price recovery and considers whether evidence indicating the cost of the investment is recoverable outweighs evidence to the contrary. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. The Company did not hold any securities with other-than-temporary impairment at December 31, 2013.
	There were no sales of available-for-sale securities during the year ended December 31, 2013. The proceeds from maturities and sales of available-for-sale securities were approximately $89.8 million and approximately $51.0 million for the year ended December 31, 2012, respectively, and approximately $212.3 million and approximately $10.0 million for the year ended December 31, 2011, respectively. Gross realized gains and losses on the sales of available-for-sale securities that have been included in other income (expense), net unrealized holding gains or losses for the period that have been included in accumulated other comprehensive income as well as gains and losses reclassified out of accumulated other comprehensive income into other income (expense) were not material to the Company's consolidated results of operations. The cost of securities sold or the amount reclassified out of the accumulated other comprehensive income into other income (expense) is based on the specific identification method for purposes of recording realized gains and losses.

Inventory

Inventory	12 Months Ended
	Dec. 31, 2013
Inventory	'
Inventory	'
	7. Inventory
	Inventory consisted of the following (in thousands):
		December 31,
		2013		2012
	Raw materials	$	22,145	$	6,699
	In the third quarter of 2012, the Company began capitalizing inventory costs for linaclotide manufactured in preparation for its launch in the U.S. and Europe based on its evaluation of, among other factors, the status of the LINZESS NDAs in the U.S., the CHMP positive recommendation to grant marketing approval for CONSTELLA in Europe, and the ability of its third-party suppliers to successfully manufacture commercial quantities of linaclotide API, which provided the Company with reasonable assurance that the net realizable value of the inventory would be recoverable. As of December 31, 2012, the previously expensed commercial API inventory was substantially utilized. Inventory at December 31, 2013 and 2012 represents API that is available for commercial sale.

Property_and_Equipment

Property and Equipment	12 Months Ended
	Dec. 31, 2013
Property and Equipment	'
Property and Equipment	'
	8. Property and Equipment
	Property and equipment, net consisted of the following (in thousands):
		December 31,
		2013			2012
	Manufacturing equipment	$	2,812		$	—
	Laboratory equipment		14,039			16,315
	Computer and office equipment		5,202			6,476
	Furniture and fixtures		2,365			2,449
	Software		12,352			11,047
	Construction in process		996			1,460
	Leased vehicles		4,472			—
	Leasehold improvements		36,827			36,770
			79,065			74,517
	Less accumulated depreciation and amortization		(41,689	)		(36,980	)
		$	37,376		$	37,537
	The Company has entered into capital leases for certain computer, vehicles and office equipment (Note 11). As of December 31, 2013 and 2012, the Company had approximately $5.5 million and approximately $1.4 million, respectively, of assets under capital leases with accumulated amortization balances of approximately $1.2 million and approximately $0.9 million, respectively.
	Depreciation and amortization expense of property and equipment, including equipment recorded under capital leases, was approximately $11.7 million, approximately $11.3 million, and approximately $10.0 million for the years ended December 31, 2013, 2012 and 2011, respectively.
	In October 2012, the Company entered into an amendment to its Cambridge, Massachusetts building lease, pursuant to which the term of the lease was extended by 24 months. As a result of this amendment, the Company extended on a prospective basis the period over which it amortizes its leasehold improvements.

Accrued_Expenses

Accrued Expenses	12 Months Ended
	Dec. 31, 2013
Accrued Expenses	'
Accrued Expenses	'
	9. Accrued Expenses
	Accrued expenses consisted of the following (in thousands):
		December 31,
		2013		2012
	Salaries and benefits	$	13,784	$	14,594
	Professional fees		531		1,031
	Accrued interest		856		—
	Other		3,267		5,546
		$	18,438	$	21,171

Notes_Payable

Notes Payable	12 Months Ended
	Dec. 31, 2013
Notes Payable	'
Notes Payable	'
	10. Notes Payable
	On January 4, 2013, the Company closed a private placement of $175.0 million in aggregate principal amount of notes due on or before June 15, 2024. The notes bear an annual interest rate of 11%, with interest payable March 15, June 15, September 15 and December 15 of each year (each a "Payment Date") beginning June 15, 2013. From and after March 15, 2014, the Company will make quarterly payments on the notes equal to the greater of (i) 7.5% of net sales of LINZESS in the U.S. for the preceding quarter (the "Synthetic Royalty Amount") and (ii) accrued and unpaid interest on the notes (the "Required Interest Amount"). Principal on the notes will be repaid in an amount equal to the Synthetic Royalty Amount minus the Required Interest Amount, when this is a positive number, until the principal has been paid in full. Given the principal payments on the notes are based on the Synthetic Royalty Amount, which will vary from quarter to quarter, the notes may be repaid prior to June 15, 2024, the final legal maturity date. The Company has not made any principal payments since January 4, 2013 and does not expect to make significant principal payments within twelve months following December 31, 2013. As such, the outstanding principal balance was classified as a long term liability as of December 31, 2013.
	The notes are secured solely by a security interest in a segregated bank account established to receive the required quarterly payments. Up to the amount of the required quarterly payments under the notes, Forest will deposit its quarterly profit (loss) sharing payments due to the Company under the collaboration agreement, if any, into the segregated bank account. If the funds deposited by Forest into the segregated bank account are insufficient to make a required payment of interest or principal on a particular Payment Date, the Company is obligated to deposit such shortfall out of the Company's general funds into the segregated bank account.
	The notes may be redeemed at any time prior to maturity, in whole or in part, at the option of the Company. If the applicable redemption of the notes occurred prior to January 1, 2014, the Company would have paid a redemption price equal to the greater of (i) the outstanding principal balance of the notes being redeemed or (ii) the present value, discounted at the rate on U.S. Treasury obligations with a comparable maturity to the remaining expected terms of the notes being redeemed plus 1.00%, of such principal payment amounts and interest on the outstanding principal balance, plus the accrued and unpaid interest to the redemption date on the notes being redeemed. If the applicable redemption of the notes occurs on or after January 1, 2014, the Company will pay a redemption price equal to the percentage of outstanding principal balance of the notes being redeemed specified below for the period in which the redemption occurs (plus the accrued and unpaid interest to the redemption date on the notes being redeemed):
	Payment Dates	Redemption
		Percentage
	From and including January 1, 2014 to and including December 31, 2014		112	%
	From and including January 1, 2015 to and including December 31, 2015		105.5	%
	From and including January 1, 2016 to and including December 31, 2016		102.75	%
	From and including January 1, 2017 and thereafter		100	%
	The notes contain certain covenants related to the Company's obligations with respect to the commercialization of LINZESS and the related collaboration agreement with Forest, as well as certain customary covenants, including covenants that limit or restrict the Company's ability to incur certain liens, merge or consolidate or make dispositions of assets. The notes also specify a number of events of default (some of which are subject to applicable cure periods), including, among other things, covenant defaults, other non-payment defaults, and bankruptcy and insolvency defaults. Upon the occurrence of an event of default, subject to cure periods in certain circumstances, all amounts outstanding may become immediately due and payable.
	The upfront cash proceeds of $175.0 million, less a discount of approximately $0.4 million for payment of legal fees incurred on behalf of the noteholders, were recorded as notes payable at issuance. The Company also capitalized approximately $7.3 million of debt issuance costs, which are included in prepaid expenses and other current assets and in other assets on the Company's consolidated balance sheet. The debt issuance costs and discount are being amortized over the estimated term of the obligation using the effective interest method. The repayment provisions represent embedded derivatives that are clearly and closely related to the notes and as such do not require separate accounting treatment.
	The accounting for the notes requires the Company to make certain estimates and assumptions about the future net sales of LINZESS in the U.S. LINZESS has been marketed since December 2012 and the estimates of the magnitude and timing of LINZESS net sales are subject to significant variability due to the recent product launch and the extended time period associated with the financing transaction, and thus subject to significant uncertainty. Therefore, these estimates and assumptions are likely to change as the Company gains additional experience marketing LINZESS, which may result in future adjustments to the portion of the debt that is classified as a current liability, the amortization of debt issuance costs and discounts as well as the accretion of the interest expense. Any such adjustments could be material.
	The fair value of the notes was estimated to be approximately $183.8 million as of December 31, 2013, and was determined using Level 3 inputs, including a quoted rate.

Commitments_and_Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2013
Commitments and Contingencies	'
Commitments and Contingencies	'
	11. Commitments and Contingencies
	Lease Commitments
	The Company leases its facility, offsite data storage location, vehicles and various equipment under leases that expire at varying dates through 2018. Certain of these leases contain renewal options, and require the Company to pay operating costs, including property taxes, insurance, maintenance and other operating expenses.
	As of December 31, 2013, the Company rents office and laboratory space at its corporate headquarters in Cambridge, Massachusetts under a non-cancelable operating lease, entered into in January 2007, as amended ("2007 Lease Agreement"). The 2007 Lease Agreement contains various provisions for renewal at our option and, in certain cases, free rent periods and rent escalation tied to the Consumer Price Index. The rent expense, inclusive of the escalating rent payments and free rent periods, is recognized on a straight-line basis over the lease term through January 2018. The Company maintains a letter of credit securing its obligations under the lease agreement of approximately $7.6 million, which is recorded as restricted cash. In addition to rents due under this lease, the Company is obligated to pay facilities charges, including utilities and taxes. In connection with the 2007 Lease Agreement, the Company was provided allowances totaling approximately $17.5 million as reimbursement for financing capital improvements to the facility. The reimbursement amount is recorded as deferred rent on the consolidated balance sheets and is being amortized as a reduction to rent expense over the lease term, as applicable. As of December 31, 2013, the Company was also obligated to rent a total of approximately 70,000 square feet of additional space in three equal stages commencing no later than June 1, 2014, June 1, 2015 and June 1, 2016.
	In 2013, the Company also entered into 36-month capital leases for the vehicle fleet for its field-based sales force and medical science liaisons. The capital leases expire at various times through September 2016. At December 31, 2013, the weighted average interest rate on the outstanding capital lease obligations was approximately 7.7%. In accordance with the terms of these arrangements, the Company maintains a letter of credit securing its obligations under the lease agreements of $0.5 million, which is recorded as restricted cash.
	The Company has also entered into capital leases for certain computer and office equipment. These capital leases expire at various times through June 2015. At December 31, 2013, the weighted average interest rate on the outstanding capital lease obligations was approximately 8.0%.
	At December 31, 2013, future minimum lease payments under all non-cancelable lease arrangements were as follows (in thousands):
		Operating		Capital
		Leases		Leases
	2014	$	13,072	$	1,434
	2015		14,152		1,265
	2016		15,255		2,157
	2017		15,778		—
	2018		604		—
	Total future minimum lease payments	$	58,861		4,856
	Less amounts representing interest				(583	)
	Capital lease obligations at December 31, 2013				4,273
	Less current portion of capital lease obligations				(1,139	)
	Capital lease obligations, net of current portion			$	3,134
	Rental expense under the operating leases amounted to approximately $8.8 million, approximately $7.2 million, and approximately $6.6 million for the years ended December 31, 2013, 2012 and 2011, respectively.
	Commercial Supply Commitments
	The Company has entered into multiple commercial supply agreements for the purchase of linaclotide finished drug product and API. Certain of the agreements contain minimum purchase commitments, the earliest of which commenced in 2012. As of December 31, 2013, the Company's minimum purchase requirements and other firm commitments related to the supply contracts associated with the territories not covered by the collaboration with Forest were approximately $8.7 million, approximately $5.9 million, approximately $7.9 million, approximately $7.9 million, approximately $2.5 million and approximately $5.0 million for the years ending December 31, 2014, 2015, 2016, 2017, 2018 and 2019 and thereafter, respectively. In addition, the Company and Forest are jointly obligated to make minimum purchases of linaclotide API for the territories covered by the Company's collaboration with Forest. Currently, Forest fulfills all such minimum purchase commitments and, as a result, they are excluded from the amounts above.
	Commitments Related to the Collaboration and License Agreements
	Under the collaborative agreements with Forest and AstraZeneca, the Company shares with Forest and AstraZeneca all development and commercialization costs related to linaclotide in the U.S. and China, respectively. The actual amounts that the Company pays its partners or that partners pay to the Company will depend on numerous factors outside of the Company's control, including the success of certain clinical development efforts with respect to linaclotide, the content and timing of decisions made by the regulators, the reimbursement and competitive landscape around linaclotide and our other product candidates, and other factors.
	In addition, the Company has commitments to make potential future milestone payments to third parties under certain of its license and collaboration arrangements. These milestones primarily include the commencement and results of clinical trials, obtaining regulatory approval in various jurisdictions and the future commercial success of development programs, the outcome and timing of which are difficult to predict and subject to significant uncertainty. In addition to the milestones discussed above, the Company is obligated to pay royalties on future sales, which are contingent on generating levels of sales of future products that have not been achieved and may never be achieved.
	See Note 4, "Collaboration and License Agreements," for additional information regarding the license and collaboration arrangements.
	Other Funding Commitments
	As of December 31, 2013, the Company has several on-going studies in various clinical trial stages. The Company's most significant clinical trial expenditures are to contract research organizations ("CRO"). The contracts with CROs generally are cancellable, with notice, at the Company's option and do not have any significant cancellation penalties.
	Guarantees
	As permitted under Delaware law, the Company indemnifies its officers and directors for certain events or occurrences while the officer or director is, or was, serving at the Company's request in such capacity. The maximum potential amount of future payments the Company could be required to make is unlimited; however, the Company has directors' and officers' insurance coverage that is intended to limit its exposure and enable it to recover a portion of any future amounts paid.
	The Company enters into certain agreements with other parties in the ordinary course of business that contain indemnification provisions. These typically include agreements with directors and officers, business partners, contractors, landlords, clinical sites and customers. Under these provisions, the Company generally indemnifies and holds harmless the indemnified party for losses suffered or incurred by the indemnified party as a result of the Company's activities. These indemnification provisions generally survive termination of the underlying agreement. The maximum potential amount of future payments the Company could be required to make under these indemnification provisions is unlimited. However, to date the Company has not incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. As a result, the estimated fair value of these obligations is minimal. Accordingly, the Company had no liabilities recorded for these obligations as of December 31, 2013 and 2012.
	Litigation
	From time to time, the Company is involved in various legal proceedings and claims, either asserted or unasserted, which arise in the ordinary course of business. While the outcome of these other claims cannot be predicted with certainty, management does not believe that the outcome of any of these ongoing legal matters, individually and in aggregate, will have a material adverse effect on the Company's consolidated financial statements.

Stockholders_Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2013
Stockholders' Equity	'
Stockholders' Equity	'
	12. Stockholders' Equity
	Preferred Stock
	The Company's preferred stock may be issued from time to time in one or more series, with each such series to consist of such number of shares and to have such terms as adopted by the board of directors. Authority is given to the board of directors to determine and fix such voting powers, full or limited, or no voting powers, and such designations, preferences and relative participating, optional or other special rights, and qualifications, limitation or restrictions thereof, including without limitation, dividend rights, conversion rights, redemption privileges and liquidation preferences.
	Common Stock
	The Company has designated two series of common stock, Series A Common Stock, which is referred to as "Class A Common Stock," and Series B Common Stock, which is referred to as "Class B Common Stock." All shares of common stock that were outstanding immediately prior to August 2008 were converted into shares of Class B Common Stock. The holders of Class A Common Stock and Class B Common Stock vote together as a single class. Class A Common Stock is entitled to one vote per share. Class B Common Stock is also entitled to one vote per share with the following exceptions: (1) after the completion of an initial public offering ("IPO") of the Company's stock, the holders of the Class B Common Stock are entitled to ten votes per share if the matter is an adoption of an agreement of merger or consolidation, an adoption of a resolution with respect to the sale, lease, or exchange of the Company's assets or an adoption of dissolution or liquidation of the Company, and (2) Class B common stockholders are entitled to ten votes per share on any matter if any individual, entity, or group seeks to obtain or has obtained beneficial ownership of 30% or more of the Company's outstanding shares of common stock. Class B Common Stock can be sold at any time and irrevocably converts to Class A Common Stock, on a one-for-one basis, upon sale or transfer. The Class B Common Stock is also entitled to a separate class vote for the issuance of additional shares of Class B Common Stock (except pursuant to dividends, splits or convertible securities), or any amendment, alteration or repeal of any provision of the Company's charter. All Class B Common Stock will automatically convert into Class A Common Stock upon the earliest of:
	•
	the later of (1) the first date on which the number of shares of Class B Common Stock then outstanding is less than 19,561,556 which represents 25% of the number of shares of Class B Common Stock outstanding immediately following the completion of the Company's IPO or (2) December 31, 2018;
	•
	December 31, 2038; or
	•
	a date agreed to in writing by a majority of the holders of the Class B Common Stock.
	The Company has reserved such number of shares of Class A Common Stock as there are outstanding shares of Class B Common Stock solely for the purpose of effecting the conversion of the Class B Common Stock.
	The holders of shares of Class A Common Stock and Class B Common Stock are entitled to dividends if and when declared by the board of directors. In the event that dividends are paid in the form of common stock or rights to acquire common stock, the holders of shares of Class A Common Stock shall receive Class A Common Stock or rights to acquire Class A Common Stock and the holders of shares of Class B Common Stock shall receive Class B Common Stock or rights to acquire Class B Common Stock, as applicable.
	In the event of a voluntary or involuntary liquidation, dissolution, distribution of assets, or winding up of the Company, the holders of shares of Class A Common Stock and the holders of shares of Class B Common Stock are entitled to share equally, on a per share basis, in all assets of the Company of whatever kind available for distribution to the holders of common stock.
	In February 2012, the Company sold 6,037,500 shares of its Class A common stock through a firm commitment, underwritten public offering at a price to the public of $15.09 per share. As a result of the offering, the Company received aggregate net proceeds, after underwriting discounts and commissions and other offering expenses, of approximately $85.2 million.
	During the second quarter of 2013, the Company sold 11,204,948 shares of its Class A common stock through a firm commitment, underwritten public offering at a price to the public of $13.00 per share. As a result of this offering, the Company received aggregate net proceeds, after underwriting discounts and commissions and other offering expenses, of approximately $137.8 million.

Stock_Benefit_Plans

Stock Benefit Plans	12 Months Ended
	Dec. 31, 2013
Stock Benefit Plans	'
Stock Benefit Plans	'
	13. Stock Benefit Plans
	The following table summarizes the expense recognized for share-based compensation arrangements in the consolidated statements of operations (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Employee stock options	$	17,981		$	16,582		$	10,904
	Restricted stock awards		552			429			431
	Non-employee stock options		271			60			152
	Employee stock purchase plan		995			472			215
	Stock award		30			30			30
		$	19,829		$	17,573		$	11,732
	Share-based compensation is reflected in the consolidated statements of operations as follows for the years ended December 31, 2013, 2012 and 2011 (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Research and development	$	9,178		$	9,080		$	6,071
	Selling, general and administrative		10,651			8,493			5,661
		$	19,829		$	17,573		$	11,732
	Stock Benefit Plans
	The Company has two share-based compensation plans pursuant to which awards are currently being made: the Amended and Restated 2010 Employee, Director and Consultant Equity Incentive Plan ("2010 Equity Plan") and the Amended and Restated 2010 Employee Stock Purchase Plan ("2010 Purchase Plan"). The Company also has two share-based compensation plans under which there are outstanding awards, but from which no further awards will be made: the Amended and Restated 2005 Stock Incentive Plan ("2005 Equity Plan") and the Amended and Restated 2002 Stock Incentive Plan ("2002 Equity Plan"). At December 31, 2013, there were 7,868,767 shares available for future grant under all such plans.
	2010 Equity Plan
	During 2010, the Company's stockholders approved the 2010 Equity Plan under which stock options, restricted stock, restricted stock units, and other stock-based awards may be granted to employees, officers, directors, or consultants of the Company. There were 6,000,000 shares of common stock initially reserved for issuance under the 2010 Equity Plan. The number of shares available for future grant may be increased on the first day of each fiscal year by an amount equal to the lesser of: (i) 6,600,000; (ii) 4% of the number of outstanding shares of common stock on the first day of each fiscal year; and (iii) an amount determined by the board of directors. Awards that are returned to the Company's other equity plans as a result of their expiration, cancellation, termination or repurchase are automatically made available for issuance under the 2010 Equity Plan. At December 31, 2013, there were 7,263,256 shares available for future grant under the 2010 Equity Plan.
	2010 Purchase Plan
	During 2010, the Company's stockholders approved the 2010 Purchase Plan, which gives eligible employees the right to purchase shares of common stock at the lower of 85% of the fair market value on the first or last day of an offering period. Each offering period is six months. There were 400,000 shares of common stock initially reserved for issuance pursuant to the 2010 Purchase Plan. The number of shares available for future grant under the 2010 Purchase Plan may be increased on the first day of each fiscal year by an amount equal to the lesser of: (i) 1,000,000 shares, (ii) 1% of the Class A shares of common stock outstanding on the last day of the immediately preceding fiscal year, or (iii) such lesser number of shares as is determined by the board of directors. At December 31, 2013, there were 574,658 shares available for future grant under the 2010 Purchase Plan.
	2005 Equity Plan and 2002 Equity Plan
	The 2005 Equity Plan and 2002 Equity Plan provided for the granting of stock options, restricted stock, restricted stock units, and other share-based awards to employees, officers, directors, consultants, or advisors of the Company. At December 31, 2013, there were 30,853 shares available for future grant under the 2005 Equity Plan and no shares available for future grant under the 2002 Equity Plan.
	Restricted Stock
	In 2009, the Company granted an aggregate of 515,549 shares of common stock to independent members of the board of directors under restricted stock agreements in accordance with the terms of the 2005 Equity Plan and the Company's director compensation program, effective in October 2009. 115,549 shares of this restricted common stock vested on December 31, 2009 and the remainder vested ratably over a four-year period ended December 31, 2013. In 2013, upon election of a new independent member of the Company's board of directors, the Company granted 8,333 shares of common stock in accordance with the terms of the 2010 Equity Plan and the Company's director compensation program. Of this restricted common stock, 833 shares vested on March 31, 2013 and the remainder vested ratably over the period ended December 31, 2013.
	A summary of the unvested shares of restricted stock as of December 31, 2013 is presented below:
		Shares			Weighted-Average
					Grant Date
					Fair Value
	Unvested at December 31, 2012		80,000		$	5.72
	Granted		8,333		$	14.94
	Vested		(88,333	)	$	6.59
	Forfeited		—		$	0
	Unvested at December 31, 2013		—		$	0
	Stock Options
	Stock options granted under the Company's equity plans generally have a ten-year term and vest over a period of four years, provided the individual continues to serve at the Company through the vesting dates. Options granted under all equity plans are exercisable at a price per share not less than the fair market value of the underlying common stock on the date of grant. The estimated fair value of options, including the effect of estimated forfeitures, is recognized over the vesting period of each option.
	The weighted average assumptions used to estimate the fair value of the stock options using the Black-Scholes option pricing model were as follows for the years ended December 31, 2013, 2012 and 2011:
		Years Ended December 31,
		2013			2012			2011
	Fair value of common stock	$	12.57		$	13.44		$	11.98
	Expected volatility		46.3	%		49.2	%		49.8	%
	Expected term (in years)		6.5			6.5			6.5
	Risk-free interest rate		1.6	%		1.2	%		2.4	%
	Expected dividend yield		—	%		—	%		—	%
	Prior to February 3, 2010, the Company was not publicly traded and therefore had no trading history. Therefore, the Company uses a blended volatility rate that blends its own historical volatility with that of comparable public companies. For purposes of identifying comparable companies, the Company selected publicly-traded companies that are in the biopharmaceutical industry, have products or product candidates in similar therapeutic areas and stages of nonclinical and clinical development, have sufficient trading history to derive a historic volatility rate and have similar vesting terms as the Company's options. The expected term is estimated using the "simplified method" since the Company has limited historical information to develop reasonable expectations about future exercise patterns and post-vesting employment termination behavior for its stock option grants. The risk-free interest rate used for each grant is based on a zero-coupon U.S. Treasury instrument with a remaining term similar to the expected term of the share-based award. The Company has not paid and does not anticipate paying cash dividends on its shares of common stock in the foreseeable future; therefore, the expected dividend yield is assumed to be zero.
	The Company's Class B Common Stock is issuable upon exercise of options granted prior to the closing of the Company's IPO under the 2002 Equity Plan and the 2005 Equity Plan, and Class A Common Stock is issuable upon exercise of all options granted after the closing of the Company's IPO under the Company's equity plans. At December 31, 2013, options exercisable into 7,918,040 shares of Class B Common Stock and 13,009,834 shares of Class A Common Stock were outstanding.
	Subject to approval by the board of directors, option grantees under the 2002 Equity Plan and the 2005 Equity Plan may have the right to exercise an option prior to vesting. The exercise of these shares is not substantive and as a result, the cash paid for the exercise prices is considered a deposit or prepayment of the exercise price and is recorded as a liability. Amounts received upon the exercise of these shares were not material to the consolidated financial statements at December 31, 2013 and 2012.
	The Company, from time to time, issues certain time-accelerated stock options to certain employees. The vesting of these options accelerates upon the achievement of certain performance-based milestones. If these criteria are not met, such options will vest between six and ten years after the date of grant. During the year ended December 31, 2013, 253,334 shares vested as a result of milestone or service period achievements. At December 31, 2013 and 2012, there were 570,000 and 823,334 shares, respectively, issuable under the unvested time-accelerated options. When achievement of the milestone is not deemed probable, the Company recognizes compensation expense associated with time-accelerated stock options initially over the vesting period of the respective stock option. When deemed probable of achievement, the Company expenses the remaining unrecognized compensation over the implicit service period. The Company recorded share-based compensation related to these time-accelerated options of less than $0.1 million, approximately $0.5 million and approximately $0.8 million during the years ended December 31, 2013, 2012 and 2011, respectively. At December 31, 2013, the Company had approximately $0.2 million in unrecognized share-based compensation, net of estimated forfeitures, related to these options.
	The Company also grants to certain employees performance-based options to purchase shares of common stock. These options are subject to performance-based milestone vesting. During the year ended December 31, 2013, 15,000 shares vested as a result of performance milestone achievements. The Company recorded share-based compensation related to these performance-based options of approximately $0.1 million, approximately $1.0 million and approximately $0.5 million, respectively, during the years ended December 31, 2013, 2012 and 2011. At December 31, 2013, the unrecognized share-based compensation related to these performance-based options was approximately $3.9 million.
	The following table summarizes stock option activity under the Company's share-based compensation plans, including performance-based options:
		Shares of			Weighted-			Weighted-			Aggregate
		Common			Average			Average			Intrinsic
		Stock			Exercise			Contractual			Value
		Attributable			Price			Life
		to Options
								(in years)			(in thousands)
	Outstanding at December 31, 2012		19,539,429		$	7.75			6.33		$	79,140
	Granted		3,857,370		$	12.57
	Exercised		(1,823,141	)	$	3.37
	Cancelled		(645,784	)	$	12.5
	Outstanding at December 31, 2013		20,927,874		$	8.87			6.14		$	71,616
	Vested or expected to vest at December 31, 2013		19,873,836		$	8.82			6.07		$	68,903
Exercisable at December 31, 2013(1)		11,537,396		$	6.89			4.77		$	59,014
-1
All stock options granted under the 2002 Equity Plan and the 2005 Equity Plan contain provisions allowing for the early exercise of such options into restricted stock. The exercisable shares disclosed above represent those that were vested as of December 31, 2013.
The weighted-average grant date fair value per share of options granted during the years ended December 31, 2013, 2012 and 2011 was $5.96, $6.62 and $6.21, respectively. The total intrinsic value of options exercised during the years ended December 31, 2013, 2012 and 2011 was approximately $19.7 million, approximately $8.6 million, and approximately $17.4 million, respectively. The intrinsic value was calculated as the difference between the fair value of the Company's common stock and the exercise price of the option issued.
As of December 31, 2013, there was approximately $34.8 million of unrecognized share-based compensation, net of estimated forfeitures, related to stock option grants with time-based vesting, which is expected to be recognized over a weighted average period of approximately 2.78 years. The total unrecognized share-based compensation cost will be adjusted for future changes in estimated forfeitures. There was no unrecognized share-based compensation related to restricted stock awards as of December 31, 2013.

Income_Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2013
Income Taxes	'
Income Taxes	'
	14. Income Taxes
	In general, the Company has not recorded a provision for federal or state income taxes as it has had cumulative net operating losses since inception. However, the Company recorded an approximately $3,000 provision for state taxes for the year ended December 31, 2011.
	A reconciliation of income taxes computed using the U.S. federal statutory rate to that reflected in operations follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Income tax benefit using U.S. federal statutory rate	$	(92,756	)	$	(24,692	)	$	(22,050	)
	Permanent differences		1,413			288			245
	State income taxes, net of federal benefit		(13,684	)		(3,835	)		(3,531	)
	Stock compensation		3,830			3,531			2,104
	Tax credits		(5,089	)		(10,420	)		509
	Expiring net operating losses and tax credits		—			564			803
	Effect of change in state tax rate on deferred tax assets and deferred tax liabilities		1,057			—			98
	Change in the valuation allowance		105,186			34,577			20,955
	Other		43			(13	)		870
		$	—		$	—		$	3
	Components of the Company's deferred tax assets and liabilities are as follows (in thousands):
		December 31,
		2013			2012
	Deferred tax assets:
	Net operating loss carryforwards	$	231,660		$	127,928
	Tax credit carryforwards		29,533			24,444
	Capitalized research and development		11,939			17,305
	Deferred revenue		6,433			8,300
	Other		29,223			25,036
	Total deferred tax assets		308,788			203,013
	Valuation allowance		(308,788	)		(203,013	)
	Net deferred tax asset	$	—		$	—
	Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets. Management has considered the Company's history of operating losses and concluded, in accordance with the applicable accounting standards, that it is more likely than not that the Company may not realize the benefit of its deferred tax assets. Accordingly, the deferred tax assets have been fully reserved at December 31, 2013 and 2012. Management reevaluates the positive and negative evidence on a quarterly basis.
	The valuation allowance increased approximately $105.8 million during the year ended December 31, 2013, due primarily to the increase in the net operating loss carryforwards and tax credits. The valuation allowance increased approximately $34.8 million during the year ended December 31, 2012, due primarily to the increase in the net operating loss carryforwards and tax credits.
	Subject to the limitations described below at December 31, 2013 and 2012, the Company has net operating loss carryforwards of approximately $600.9 million and approximately $334.1 million, respectively, to offset future federal taxable income, which expire beginning in 2018 continuing through 2033. The federal net operating loss carryforwards exclude approximately $37.3 million of deductions related to the exercise of stock options. This amount represents an excess tax benefit and has not been included in the gross deferred tax asset reflected for net operating losses. This amount will be recorded as an increase in additional paid in capital on the consolidated balance sheet once the excess benefits are "realized" in accordance with ASC 718. As of December 31, 2013 and 2012, the Company has state net operating loss carryforwards of approximately $545.3 million and approximately $271.4 million, respectively, to offset future state taxable income, which have begun to expire and will continue to expire through 2033. The Company also has tax credit carryforwards of approximately $32.1 million and approximately $26.4 million as of December 31, 2013 and 2012, respectively, to offset future federal and state income taxes, which expire at various times through 2033.
	Utilization of net operating loss carryforwards and research and development credit carryforwards may be subject to a substantial annual limitation due to ownership change limitations that have occurred previously or that could occur in the future in accordance with Section 382 of the Internal Revenue Code of 1986 ("IRC Section 382") and with Section 383 of the Internal Revenue Code of 1986, as well as similar state provisions. These ownership changes may limit the amount of net operating loss carryforwards and research and development credit carryforwards that can be utilized annually to offset future taxable income and taxes, respectively. In general, an ownership change, as defined by IRC Section 382, results from transactions increasing the ownership of certain stockholders or public groups in the stock of a corporation by more than 50 percentage points over a three-year period. The Company has completed several financings since its inception which may have resulted in a change in control as defined by IRC Section 382, or could result in a change in control in the future.
	The Company applies ASC 740, Income Taxes. ASC 740 provides guidance on the accounting for uncertainty in income taxes recognized in financial statements and requires the impact of a tax position to be recognized in the financial statements if that position is more likely than not of being sustained by the taxing authority. As a result of the implementation of the new guidance, the Company recognized no material adjustment for unrecognized income tax benefits. At December 31, 2013 and 2012, the Company had no unrecognized tax benefits.
	The Company will recognize interest and penalties related to uncertain tax positions in income tax expense. As of December 31, 2013, 2012 and 2011, the Company had no accrued interest or penalties related to uncertain tax positions and no amounts have been recognized in the Company's consolidated statements of operations.
	The statute of limitations for assessment by the Internal Revenue Service ("IRS") and state tax authorities is open for tax years ended December 31, 2012, 2011 and 2010, although carryforward attributes that were generated prior to tax year 2011 may still be adjusted upon examination by the IRS or state tax authorities if they either have been, or will be, used in a future period. There are currently no federal or state income tax audits in progress.
	During 2012, the Company completed a study of its research and development credit carryforwards for the years 2003 through 2011. This study resulted in an increase in the Company's research and development credit carryforwards of approximately $9.9 million. These research and development credit carryforwards are subject to a full valuation allowance.

Defined_Contribution_Plan

Defined Contribution Plan	12 Months Ended
	Dec. 31, 2013
Defined Contribution Plan	'
Defined Contribution Plan	'
	15. Defined Contribution Plan
	The Ironwood Pharmaceuticals, Inc. 401(k) Savings Plan is a defined contribution plan in the form of a qualified 401(k) plan in which substantially all employees are eligible to participate upon employment. Subject to certain IRS limits, eligible employees may elect to contribute from 1% to 100% of their compensation. Company contributions to the plan are at the sole discretion of the Company's board of directors. Currently, the Company provides a matching contribution of 75% of the employee's contributions, up to $6,000 annually. During the years ended December 31, 2013, 2012 and 2011, the Company recorded approximately $2.8 million, approximately $1.9 million and approximately $0.6 million of expense related to its 401(k) company match, respectively.

Related_Party_Transactions

Related Party Transactions	12 Months Ended
	Dec. 31, 2013
Related Party Transactions	'
Related Party Transactions	'
	16. Related Party Transactions
	The Company has and currently obtains legal services from a law firm that is an investor of the Company. The Company paid approximately $0.1 million, approximately $0.2 million and approximately $0.2 million in legal fees to this investor during the years ended December 31, 2013, 2012 and 2011, respectively. At both December 31, 2013 and 2012, the Company had less than $0.1 million of accounts payable due to this related party.
	In September 2009, Forest became a related party when the Company sold to Forest 2,083,333 shares of the Company's convertible preferred stock and in November 2009, Almirall became a related party when the Company sold to Almirall 681,819 shares of the Company's convertible preferred stock (Note 4). These shares of preferred stock converted to the Company's Class B common stock on a 1:1 basis upon the completion of the Company's IPO in February 2010. Amounts due to and due from Forest and Almirall are reflected as related party accounts payable and related party accounts receivable, respectively. These balances are reported net of any balances due to or from the related party. At December 31, 2013, the Company had less than $0.1 million in related party accounts receivable associated with Almirall and approximately $2.7 million in related party accounts receivable, net of related party accounts payable, associated with Forest. At December 31, 2012, the Company had approximately $1.0 million in related party accounts receivable associated with Almirall and approximately $7.5 million in related party accounts payable, net of related party accounts receivable, associated with Forest.

State_Grants

State Grants	12 Months Ended
	Dec. 31, 2013
State Grants	'
State Grants	'
	17. State Grants
	In the years ended December 31, 2012 and 2011, the Company was awarded an approximately $1.7 million and approximately $0.9 million tax incentive, respectively, associated with the Life Sciences Tax Incentive Program from the Massachusetts Life Sciences Center. The program was established in 2008 in order to incentivize life sciences companies to create new sustained jobs in Massachusetts. Jobs must be maintained for at least five years, during which time the grant proceeds can be recovered by the Massachusetts Department of Revenue ("DOR") if the Company does not meet and maintain its job creation commitments. The award received in July 2011 was recognized as other income in the consolidated statement of operations in the third quarter of 2011, as the Company believed it had satisfied its job creation commitments. The $1.7 million in funds received in 2012 are recorded as other liabilities and no amount has been recognized in the statement of operations through December 31, 2013.

Selected_Quarterly_Financial_D

Selected Quarterly Financial Data (Unaudited)	12 Months Ended
	Dec. 31, 2013
Selected Quarterly Financial Data (Unaudited)	'
Selected Quarterly Financial Data (Unaudited)	'
	18. Selected Quarterly Financial Data (Unaudited)
	The following table contains quarterly financial information for the years ended December 31, 2013 and 2012. The Company believes that the following information reflects all normal recurring adjustments necessary for a fair presentation of the information for the periods presented. The operating results for any quarter are not necessarily indicative of results for any future period.
		First			Second			Third			Fourth			Total
		Quarter			Quarter			Quarter			Quarter			Year
		(in thousands, except per share data)
	2013
	Collaborative arrangements revenue	$	3,255		$	9,663		$	4,932		$	5,031		$	22,881
	Total cost and expenses		92,088			69,543			61,483			51,769			274,883
	Other income (expense), net		(5,069	)		(5,269	)		(5,224	)		(5,248	)		(20,810	)
	Net loss		(93,902	)		(65,149	)		(61,775	)		(51,986	)		(272,812	)
	Net loss per share—basic and diluted	$	(0.87	)	$	(0.57	)	$	(0.51	)	$	(0.43	)	$	(2.35	)
		First			Second			Third			Fourth			Total
		Quarter			Quarter			Quarter			Quarter			Year
		(in thousands, except per share data)
	2012
	Collaborative arrangements revenue	$	12,248		$	14,604		$	96,413		$	26,980		$	150,245
	Total cost and expenses		47,884			55,438			48,805			70,880			223,007
	Other income (expense), net		35			31			27			45			138
	Net income (loss)		(35,601	)		(40,803	)		47,635			(43,855	)		(72,624	)
	Basic net income (loss) per share	$	(0.34	)	$	(0.38	)	$	0.44		$	(0.41	)	$	(0.68	)
	Diluted net income (loss) per share	$	(0.34	)	$	(0.38	)	$	0.42		$	(0.41	)	$	(0.68	)

Subsequent_Events

Subsequent Events	12 Months Ended
	Dec. 31, 2013
Subsequent Events	'
Subsequent Events	'
	19. Subsequent Events
	On January 8, 2014, the Company announced a headcount reduction of approximately 10% to align its workforce with its strategy to grow a leading GI therapeutics company. As maximizing LINZESS is core to the Company's strategy, its field-based sales force and medical science liaison team were excluded from the workforce reduction. The Company estimates that it will incur aggregate charges in connection with its reduction in workforce of approximately $4.0 million to $4.5 million for employee severance and benefit costs, of which approximately 85% to 95% are expected to result in cash expenditures. The Company committed to this course of action on January 8, 2014, and expects to complete the reduction in workforce during the first quarter of 2014.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2013

Summary of Significant Accounting Policies

'

Principles of Consolidation

'

Principles of Consolidation

The accompanying consolidated financial statements include the accounts of Ironwood Pharmaceuticals, Inc. and its wholly owned subsidiaries, Ironwood Pharmaceuticals Securities Corporation and Ironwood Pharmaceuticals GmbH. All intercompany transactions and balances are eliminated in consolidation.

Use of Estimates

'

Use of Estimates

The preparation of consolidated financial statements in accordance with generally accepted accounting principles in the U.S. requires the Company's management to make estimates and judgments that may affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosure of contingent assets and liabilities. On an on-going basis, the Company's management evaluates its estimates, including those related to revenue recognition, available-for-sale securities, inventory valuation and related reserves, impairment of long-lived assets, balance sheet classification of notes payable, income taxes including the valuation allowance for deferred tax assets, research and development expense, contingencies and share-based compensation. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known.

Cash and Cash Equivalents

'

Cash and Cash Equivalents

The Company considers all highly liquid investment instruments with a remaining maturity when purchased of three months or less to be cash equivalents. Investments qualifying as cash equivalents primarily consist of money market funds and U.S. government-sponsored securities. The carrying amount of cash equivalents approximates fair value. The amount of cash equivalents included in cash and cash equivalents was approximately $67.3 million and approximately $113.9 million at December 31, 2013 and 2012, respectively.

Restricted Cash

'

Restricted Cash

The Company is contingently liable under unused letters of credit with a bank, related to the Company's facility and automobile lease agreements and credit card arrangements, in the amount of approximately $8.1 million and approximately $7.6 million as of December 31, 2013 and 2012, respectively. As a result, the Company has restricted cash of approximately $8.1 million and approximately $7.6 million as of December 31, 2013 and 2012, respectively, securing these letters of credit. The cash will be restricted until the termination of the leases and credit card arrangements.

Available-for-Sale Securities

'

Available-for-Sale Securities

The Company classifies all short-term investments with a remaining maturity when purchased of greater than three months as available-for-sale. Available-for-sale securities are recorded at fair value, with the unrealized gains and losses reported in other comprehensive income (loss). The amortized cost of debt securities in this category is adjusted for the amortization of premiums and accretion of discounts to maturity. Such amortization is included in interest and investment income. Realized gains and losses, interest, dividends, and declines in value judged to be other than temporary on available-for-sale securities are included in interest and investment income.

The cost of securities sold is based on the specific identification method for purposes of recording realized gains and losses. To determine whether an other-than-temporary impairment exists, the Company considers whether it has the ability and intent to hold the investment until a market price recovery, and whether evidence indicating the recoverability of the cost of the investment outweighs evidence to the contrary. There were no other-than-temporary impairments for the years ended December 31, 2013, 2012 and 2011.

Inventory

'

Inventory

Inventory is stated at the lower of cost or market with cost determined under the first-in, first-out basis.

The Company evaluates inventory levels quarterly and any inventory that has a cost basis in excess of its expected net realizable value, inventory that becomes obsolete, inventory in excess of expected sales requirements or inventory that fails to meet commercial sale specifications is written down with a corresponding charge to cost of revenue in the period that the impairment is first identified.

The Company capitalizes inventories manufactured in preparation for initiating sales of a product candidate when the related product candidate is considered to have a high likelihood of regulatory approval and the related costs are expected to be recoverable through sales of the inventories. In determining whether or not to capitalize such inventories, the Company evaluates, among other factors, information regarding the product candidate's safety and efficacy, the status of regulatory submissions and communications with regulatory authorities and the outlook for commercial sales, including the existence of current or anticipated competitive drugs and the availability of reimbursement. In addition, the Company evaluates risks associated with manufacturing the product candidate, including the ability of the Company's third-party suppliers to complete the validation batches, and the remaining shelf life of the inventories.

Costs associated with developmental products prior to satisfying the inventory capitalization criteria are charged to research and development expense as incurred.

Concentrations of Suppliers

'

Concentrations of Suppliers

The Company relies on third-party manufacturers and its collaboration partners to manufacture the linaclotide active pharmaceutical ingredient ("API") and final linaclotide drug product. Currently, there are two third-party manufacturers approved for the production of the linaclotide API in three facilities. The Company's collaboration partners, except AstraZeneca in China, (Forest, Almirall and Astellas) are responsible for drug product manufacturing of linaclotide into finished product for their respective territories. The Company also has an agreement with another independent third party to serve as a second source of drug product manufacturing of linaclotide for its partnered territories. The Company and AstraZeneca also continue to explore manufacturing alternatives for China. If any of the Company's suppliers were to limit or terminate production or otherwise fail to meet the quality or delivery requirements needed to satisfy the supply commitments, the process of locating and qualifying alternate sources could require up to several months, during which time the Company's production could be delayed. Such delays could have a material adverse effect on the Company's business, financial position and results of operations.

Accounts Receivable and Related Valuation Account

'

Accounts Receivable and Related Valuation Account

The Company makes judgments as to its ability to collect outstanding receivables and provides an allowance for receivables when collection becomes doubtful. Provisions are made based upon a specific review of all significant outstanding invoices and the overall quality and age of those invoices not specifically reviewed. The Company's receivables primarily relate to amounts reimbursed under its collaboration and license agreements. The Company believes that credit risks associated with these collaborators are not significant. To date, the Company has not had any write-offs of bad debt, and as such, the Company does not have an allowance for doubtful accounts as of December 31, 2013 and 2012.

Concentrations of Credit Risk

'

Concentrations of Credit Risk

Financial instruments that subject the Company to credit risk primarily consist of cash and cash equivalents, restricted cash, available-for-sale securities, and accounts receivable. The Company maintains its cash and cash equivalent balances with high-quality financial institutions and, consequently, the Company believes that such funds are subject to minimal credit risk. The Company's available-for-sale investments primarily consist of U.S. Treasury securities and certain U.S. government sponsored securities and potentially subject the Company to concentrations of credit risk. The Company has adopted an investment policy which limits the amounts the Company may invest in any one type of investment, and requires all investments held by the Company to be at least A+ rated, thereby reducing credit risk exposure.

Accounts receivable, including related party accounts receivable, primarily consist of amounts due under the collaboration agreement with Forest and license agreement with Astellas (Note 4) for which the Company does not obtain collateral. Accounts receivable or payable to or from Forest and Almirall are presented as related party transactions on the consolidated balance sheets as both entities own common stock of the Company.

The percentages of revenue recognized from significant customers of the Company in the years ended December 31, 2013, 2012 and 2011 as well as the account receivable balances, net of any payables due, at December 31, 2013 and 2012 are included in the following table:

Accounts Receivable

Revenue

December 31,

Years Ended December 31,

2013

2012

2013

2012

2011

Collaborative Partner:

Forest

84

%

—

%

13

%

67

%

64

%

Almirall

—

%

69

%

57

%

14

%

31

%

Astellas

16

%

31

%

25

%

3

%

5

%

AstraZeneca

—

%

—

%

5

%

16

%

—

%

As of December 31, 2013, the Company was in a net payable position with AstraZeneca; as such, there was no accounts receivable due from AstraZeneca as of December 31, 2013. As of December 31, 2012, the Company was in a net payable position with Forest; as such, there was no accounts receivable due from Forest as of December 31, 2012.

For the years ended December 31, 2013, 2012 and 2011, no additional customers accounted for more than 10% of the Company's revenue.

Revenue Recognition

'

Revenue Recognition

The Company's revenue is generated through collaborative research and development and licensing agreements. The terms of these agreements contain multiple deliverables which may include (i) licenses, (ii) research and development activities, including participation on joint steering committees, and (iii) the manufacture of finished drug product, API, or development materials for the collaborative partner which are reimbursed at a contractually determined rate. Non-refundable payments to the Company under these agreements may include (i) up-front license fees, (ii) payments for research and development activities, (iii) payments for the manufacture of finished drug product, API, or development materials, (iv) payments based upon the achievement of certain milestones, and (v) royalties on product sales. Additionally, the Company may receive its share of the net profits or bear its share of the net losses from the sale of linaclotide in the U.S. and China through its collaborations with Forest and AstraZeneca, respectively.

At December 31, 2013, the Company had collaboration agreements with Forest and AstraZeneca and license agreements with Almirall and Astellas. Refer to Note 4, "Collaboration and License Agreements," for additional discussion of these agreements.

The Company recognizes revenue when there is persuasive evidence that an arrangement exists, services have been rendered or delivery has occurred, the price is fixed or determinable, and collection is reasonably assured.

For certain of our arrangements, particularly the license agreement with Almirall, it is required that taxes be withheld on payments to the Company. The Company has adopted a policy to recognize revenue net of these tax withholdings.

Agreements Entered into Prior to January 1, 2011

For arrangements that include multiple deliverables, the Company follows the provisions of the Accounting Standards Codification ("ASC") Topic 605-25, Revenue Recognition—Multiple-Element Arrangements ("ASC 605-25"), in accounting for these agreements. Under ASC 605-25, the Company was required to identify the deliverables included within the agreement and evaluate which deliverables represent separate units of accounting. Collaborative research and development and licensing agreements that contained multiple deliverables were divided into separate units of accounting when the following criteria were met:

•

Delivered element(s) had value to the collaborator on a standalone basis,

•

There was objective and reliable evidence of the fair value of the undelivered obligation(s), and

•

If the arrangement included a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) was considered probable and substantially within the Company's control.

The Company allocated arrangement consideration among the separate units of accounting either on the basis of each unit's respective fair value or using the residual method, and applied the applicable revenue recognition criteria to each of the separate units. If the separation criteria were not met, revenue of the combined unit of accounting was recorded based on the method appropriate for the last delivered item.

Up-Front License Fees

The Company recognizes revenue from nonrefundable, up-front license fees on a straight-line basis over the contracted or estimated period of performance, which is typically the period over which the research and development is expected to occur or manufacturing services are expected to be provided. Accordingly, the Company is required to make estimates regarding the drug development and commercialization timelines for drugs and drug candidates being developed pursuant to the applicable agreement. The determination of the length of the period over which to recognize the revenue is subject to judgment and estimation and can have an impact on the amount of revenue recognized in a given period. Quarterly, the Company reassesses its period of substantial involvement over which the Company amortizes its up-front license fees and makes adjustments as appropriate. The Company's estimates regarding the period of performance under its collaborative research and development and licensing agreements have changed in the past and may change in the future. In the event that a license were to be terminated, the Company would recognize as revenue any portion of the up-front fee that had not previously been recorded as revenue, but was classified as deferred revenue at the date of such termination. At December 31, 2013, only a portion of Astellas' up-front license fee remains deferred as the period of performance under the Forest and Almirall arrangements ended in the quarter ended September 30, 2012.

Agreements Entered into or Materially Modified on or after January 1, 2011

The Company evaluates revenue from new multiple element agreements entered into on or after January 1, 2011 under ASU No. 2009-13, Multiple-Deliverable Revenue Arrangements ("ASU 2009-13"), which was adopted on a prospective basis in January 2011. The Company also evaluates whether amendments to its multiple element arrangements are considered material modifications that are subject to the application of ASU 2009-13. This evaluation requires management to assess all relevant facts and circumstances and to make subjective determinations and judgments. As part of this assessment, the Company considers whether the modification results in a material change to the arrangement, including whether there is a change in total arrangement consideration that is more than insignificant, whether there are changes in the deliverables included in the arrangement, whether there is a change in the term of the arrangement and whether there is a significant modification to the delivery schedule for contracted deliverables.

When evaluating multiple element arrangements under ASU 2009-13, the Company considers whether the deliverables under the arrangement represent separate units of accounting. This evaluation requires subjective determinations and requires management to make judgments about the individual deliverables and whether such deliverables are separable from the other aspects of the contractual relationship. In determining the units of accounting, management evaluates certain criteria, including whether the deliverables have standalone value, based on the consideration of the relevant facts and circumstances for each arrangement. Factors considered in this determination include the research, manufacturing and commercialization capabilities of the partner and the availability of peptide research and manufacturing expertise in the general marketplace. In addition, the Company considers whether the collaborator can use the license or other deliverables for their intended purpose without the receipt of the remaining elements, and whether the value of the deliverable is dependent on the undelivered items and whether there are other vendors that can provide the undelivered items.

The consideration received is allocated among the separate units of accounting using the relative selling price method, and the applicable revenue recognition criteria are applied to each of the separate units.

The Company determines the estimated selling price for deliverables using vendor-specific objective evidence ("VSOE") of selling price, if available, third-party evidence ("TPE") of selling price if VSOE is not available, or best estimate of selling price ("BESP") if neither VSOE nor TPE is available. Determining the BESP for a deliverable requires significant judgment. The Company uses BESP to estimate the selling price for licenses to the Company's proprietary technology, since the Company often does not have VSOE or TPE of selling price for these deliverables. In those circumstances where the Company utilizes BESP to determine the estimated selling price of a license to the Company's proprietary technology, the Company considers market conditions as well as entity-specific factors, including those factors contemplated in negotiating the agreements as well as internally developed models that include assumptions related to the market opportunity, estimated development costs, probability of success and the time needed to commercialize a product candidate pursuant to the license. In validating the Company's BESP, the Company evaluates whether changes in the key assumptions used to determine the BESP will have a significant effect on the allocation of arrangement consideration between multiple deliverables.

At December 31, 2013, the Company has one collaboration agreement with AstraZeneca that is being accounted for under ASU 2009-13.

Up-Front License Fees

When management believes the license to its intellectual property has stand-alone value, the Company generally recognizes revenue attributed to the license upon delivery. When management believes the license to its intellectual property does not have stand-alone value from the other deliverables to be provided in the arrangement, it is combined with other deliverables and the revenue of the combined unit of accounting is recorded based on the method appropriate for the last delivered item.

Milestones

At the inception of each arrangement that includes pre-commercial milestone payments, the Company evaluates whether each pre-commercial milestone is substantive, in accordance with ASU No. 2010-17, Revenue Recognition—Milestone Method ("ASU 2010-17"), adopted on January 1, 2011. This evaluation includes an assessment of whether (a) the consideration is commensurate with either (1) the entity's performance to achieve the milestone, or (2) the enhancement of the value of the delivered item(s) as a result of a specific outcome resulting from the entity's performance to achieve the milestone, (b) the consideration relates solely to past performance and (c) the consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. The Company evaluates factors such as the scientific, clinical, regulatory, commercial and other risks that must be overcome to achieve the respective milestone, the level of effort and investment required and whether the milestone consideration is reasonable relative to all deliverables and payment terms in the arrangement in making this assessment. At December 31, 2013, the Company had no pre-commercial milestones that were deemed substantive. If a substantive pre-commercial milestone is achieved and collection of the related receivable is reasonably assured, the Company recognizes revenue related to the milestone in its entirety in the period in which the milestone is achieved. If the Company were to achieve milestones that are considered substantive under any of the Company's collaborations, the Company may experience significant fluctuations in collaborative arrangements revenue from quarter to quarter and year to year depending on the timing of achieving such substantive milestones. In those circumstances where a pre-commercial milestone is not substantive, the Company recognizes as revenue on the date the milestone is achieved an amount equal to the applicable percentage of the performance period that had elapsed as of the date the milestone was achieved, with the balance being deferred and recognized over the remaining period of performance. Pre-commercial milestone payments received prior to the adoption of ASU 2010-17 continue to be recognized over the remaining period of performance.

Commercial milestones are accounted for as royalties and are recorded as revenue upon achievement of the milestone, assuming all other revenue recognition criteria are met.

Net Profit or Net Loss Sharing

In accordance with ASC 808 Topic, Collaborative Arrangements, and ASC 605-45, Principal Agent Considerations, the Company considers the nature and contractual terms of the arrangement and the nature of the Company's business operations to determine the classification of the transactions under the Company's collaboration agreements. The Company records revenue transactions gross in the consolidated statements of operations if it is deemed the principal in the transaction, which includes being the primary obligor and having the risks and rewards of ownership.

The Company recognizes its share of the pre-tax commercial net profit or net loss generated from the sales of LINZESS in the U.S. in the period the product sales are reported by Forest and related cost of goods sold and selling, general and administrative expenses are incurred by the Company and its collaboration partner. These amounts are partially determined based on amounts provided by Forest and involve the use of estimates and judgments, such as product sales allowances and accruals related to prompt payment discounts, chargebacks, governmental and contractual rebates, wholesaler fees, product returns, and co-payment assistance costs, which could be adjusted based on actual results in the future. The Company is highly dependent on Forest for timely and accurate information regarding any net revenues realized from sales of LINZESS and the costs incurred in selling it, in order to accurately report its results of operations. For the periods covered in the consolidated financial statements presented, there have been no material changes to prior period estimates of revenues, cost of goods sold or selling, general and administrative expenses associated with the sales of LINZESS in the U.S. However, if the Company does not receive timely and accurate information or incorrectly estimates activity levels associated with the collaboration at a given point in time, the Company could be required to record adjustments in future periods.

The Company records its share of the net profits or net losses from the sales of LINZESS in the U.S. on a net basis and presents the settlement payments to and from Forest as collaboration expense or collaborative arrangements revenue, as applicable, as the Company is not the primary obligor and does not have the risks and rewards of ownership in the collaboration agreement with Forest. The Company and Forest settle the cost sharing quarterly, such that the Company's statement of operations reflects 50% of the pre-tax net profit or loss generated from sales of LINZESS in the U.S. Prior to the fourth quarter of 2012, selling, general and administrative cost-sharing payments were presented within selling, general and administrative expenses. The cost-sharing payments to Forest for the nine months ended September 30, 2012 were reclassified to conform to the current period's presentation. Prior to 2012, such selling, general and administrative cost-sharing payments were presented within selling, general and administrative expenses and were not material to the consolidated financial statements.

Royalties on Product Sales

The Company receives or expects to receive in the future royalty revenues under certain of the Company's license or collaboration agreements. If the Company does not have any future performance obligations under these license or collaborations agreements, the Company records these revenues as earned. To the extent the Company does not have access to the royalty reports from the Company's partners or the ability to accurately estimate the royalty revenue in the period earned, the Company records such royalty revenues one quarter in arrears.

Other

The Company produces finished drug product, API and development materials for certain of its collaborators. The Company recognizes revenue on finished drug product, API and development materials when the material has passed all quality testing required for collaborator acceptance, delivery has occurred, title and risk of loss have transferred to the collaborator, the price is fixed or determinable, and collection is reasonably assured. As it relates to development materials and API produced for Almirall and Astellas, the Company is reimbursed at a contracted rate. Such reimbursements are considered as part of revenue generated pursuant to the Almirall and Astellas license agreements and are presented as collaborative arrangements revenue. Any finished drug product, API and development materials currently produced for Forest or AstraZeneca are recognized in accordance with the cost-sharing provisions of the Forest and AstraZeneca collaboration agreements, respectively.

Cost of Revenue

'

Cost of Revenue

Cost of revenue is recognized upon shipment of linaclotide API to certain of the Company's collaboration partners and consists of the costs of producing such API. The costs of API were primarily recorded as research and development expenses in the periods prior to July 1, 2012. In the third quarter of 2012, the Company began capitalizing inventory costs for linaclotide API manufactured in preparation for its launch of linaclotide in the U.S. and Europe based on its evaluation of, among other factors, the status of the LINZESS NDAs in the U.S., the Committee for Medicinal Products for Human Use ("CHMP") positive recommendation to grant marketing approval for CONSTELLA in Europe, and the ability of the Company's third-party suppliers to successfully manufacture commercial quantities of linaclotide API, which provided the Company with reasonable assurance that the net realizable value of the inventory would be recoverable. As of December 31, 2012, the previously expensed commercial API inventory was substantially utilized.

Research and Development Costs

'

Research and Development Costs

The Company expenses research and development costs to operations as incurred. The Company defers and capitalizes nonrefundable advance payments made by the Company for research and development activities until the related goods are received or the related services are performed.

Research and development expenses are comprised of costs incurred in performing research and development activities, including salary, benefits and other employee-related expenses; share-based compensation expense; laboratory supplies and other direct expenses; facilities expenses; overhead expenses; third-party contractual costs relating to nonclinical studies and clinical trial activities and related contract manufacturing expenses, development of manufacturing processes and regulatory registration of third-party manufacturing facilities; costs associated with linaclotide API prior to the Company concluding that regulatory approval is probable and that its net realizable value is recoverable; licensing fees for our product candidates; and other outside expenses.

The Company has entered into collaboration agreements with Forest and AstraZeneca pursuant to which it shares research and development expenses with the collaborators. The Company records expenses incurred under the collaboration arrangements for such work as research and development expense. Because the collaboration arrangements are cost-sharing arrangements, the Company concluded that when there is a period during the collaboration arrangements during which the Company receives payments from Forest or AstraZeneca, the Company records the payments by Forest or AstraZeneca for their share of the development effort as a reduction of research and development expense. Payments to Forest or AstraZeneca are recorded as incremental research and development expense.

Selling, General and Administrative Expenses

'

Selling, General and Administrative Expenses

The Company expenses selling, general and administrative costs to operations as incurred. Selling, general and administrative expense consists primarily of compensation, benefits and other employee-related expenses for personnel in our administrative, finance, legal, information technology, business development, commercial, sales, marketing, communications and human resource functions. Other costs include the legal costs of pursuing patent protection of the Company's intellectual property, general and administrative related facility costs and professional fees for accounting and legal services.

Under the Forest and AstraZeneca collaboration agreements, the Company is reimbursed for certain selling, general and administrative expenses and it nets these reimbursements against selling, general and administrative expenses as incurred. Payments to Forest or AstraZeneca are recorded as incremental selling, general and administrative expense.

Beginning in the fourth quarter of 2012, the Company includes Forest's selling, general and administrative cost-sharing payments in the calculation of the net profits and net losses from the sale of LINZESS in the U.S. and presents the net payment to or from Forest as collaboration expense or collaborative arrangements revenue, as applicable. The selling, general and administrative cost-sharing payments to Forest for the nine months ended September 30, 2012 were reclassified to conform to the current presentation. Prior to 2012, such Forest-related selling, general and administrative cost-sharing payments were presented within selling, general and administrative expenses and were not material to the consolidated financial statements.

Share-Based Compensation

'

Share-Based Compensation

The Company's stock-based compensation programs grant awards which have included stock awards, restricted stock, and stock options. Share-based compensation is recognized as an expense in the financial statements based on the grant date fair value over the requisite service period. For awards that vest based on service conditions, the Company uses the straight-line method to allocate compensation expense to reporting periods. The grant date fair value of options granted is calculated using the Black-Scholes option-pricing model, which requires the use of subjective assumptions including volatility and expected term, among others.

The Company records the expense for stock option grants subject to performance-based milestone vesting using the accelerated attribution method over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates when the achievement of a performance-based milestone is probable based on the relative satisfaction of the performance conditions as of the reporting date.

The Company records the expense of services rendered by non-employees based on the estimated fair value of the stock option using the Black-Scholes option-pricing model. The fair value of unvested non-employee awards is remeasured at each reporting period and expensed over the vesting term of the underlying stock options.

Patent Costs

'

Patent Costs

The Company incurred and recorded as operating expense legal and other fees related to patents of approximately $3.2 million, approximately $3.5 million, and approximately $2.2 million for the years ended December 31, 2013, 2012 and 2011, respectively. These costs were charged to selling, general and administrative expenses as incurred.

Net Income (Loss) Per Share

'

Net Income (Loss) Per Share

The Company calculates basic net income (loss) per common share and diluted net loss per common share by dividing the net income (loss) by the weighted average number of common shares outstanding during the period. Diluted net income per common share is computed by dividing net income by the diluted number of shares outstanding during the period. Except where the result would be antidilutive to net income, diluted net income per share is computed assuming the exercise of common stock options and the vesting of restricted stock (using the treasury stock method), as well as their related income tax effects. The Company allocates undistributed earnings between the classes on a one-to-one basis when computing net income (loss) per share. As a result, basic and diluted net income (loss) per Class A and Class B shares are equivalent.

Property and Equipment

'

Property and Equipment

Property and equipment, including leasehold improvements, are recorded at cost, and are depreciated when placed into service using the straight-line method based on their estimated useful lives as follows:

Asset Description

Estimated Useful Life

(In Years)

Manufacturing equipment

10

Laboratory equipment

5

Computer and office equipment

3

Furniture and fixtures

7

Software

3

Included in property and equipment are certain costs of software obtained for internal use. Costs incurred during the preliminary project stage are expensed as incurred, while costs incurred during the application development stage are capitalized and amortized over the estimated useful life of the software. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditures will result in additional functionality. Maintenance and training costs related to software obtained for internal use are expensed as incurred.

Leasehold improvements are amortized over the shorter of the estimated useful life of the asset or the lease term. Capital lease assets are amortized over the lease term. However, if ownership was transferred by the end of the capital lease, or there was a bargain purchase option, such capital lease assets would be amortized over the useful life that would be assigned if such assets were owned.

Costs for capital assets not yet placed into service have been capitalized as construction in progress, and will be depreciated in accordance with the above guidelines once placed into service. Maintenance and repair costs are expensed as incurred.

Income Taxes

'

Income Taxes

The Company provides for income taxes under the liability method. Deferred tax assets and liabilities are determined based on differences between financial reporting and tax bases of assets and liabilities and are measured using the enacted tax rates in effect when the differences are expected to reverse. Deferred tax assets are reduced by a valuation allowance to reflect the uncertainty associated with their ultimate realization.

The Company accounts for uncertain tax positions recognized in the consolidated financial statements by prescribing a more-likely-than-not threshold for financial statement recognition and measurement of a tax position taken or expected to be taken in a tax return.

Impairment of Long-Lived Assets

'

Impairment of Long-Lived Assets

The Company regularly reviews the carrying amount of its long-lived assets to determine whether indicators of impairment may exist, which warrant adjustments to carrying values or estimated useful lives. If indications of impairment exist, projected future undiscounted cash flows associated with the asset are compared to the carrying amount to determine whether the asset's value is recoverable. If the carrying value of the asset exceeds such projected undiscounted cash flows, the asset will be written down to its estimated fair value. There were no significant impairments of long-lived assets for the years ended December 31, 2013, 2012 or 2011.

Comprehensive Income (Loss)

'

Comprehensive Income (Loss)

Comprehensive income (loss) is defined as the change in equity of a business enterprise during a period from transactions, and other events and circumstances from non-owner sources and currently consists of net loss and changes in unrealized gains and losses on available-for-sale securities.

Segment Information

'

Segment Information

Operating segments are components of an enterprise for which separate financial information is available and is evaluated regularly by the Company's chief operating decision-maker in deciding how to allocate resources and in assessing performance. The Company currently operates in one reportable business segment—human therapeutics.

New Accounting Pronouncements

'

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board or other standard setting bodies that are adopted by the Company as of the specified effective date. The Company did not adopt any new accounting pronouncements during the year ended December 31, 2013 that had a material effect on its consolidated financial statements.

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2013
Summary of Significant Accounting Policies	'
Schedule of percentages of revenue and accounts receivable recognized from significant customers	'
		Accounts Receivable						Revenue
		December 31,						Years Ended December 31,
		2013			2012			2013			2012			2011
	Collaborative Partner:
	Forest		84	%		—	%		13	%		67	%		64	%
	Almirall		—	%		69	%		57	%		14	%		31	%
	Astellas		16	%		31	%		25	%		3	%		5	%
	AstraZeneca		—	%		—	%		5	%		16	%		—	%
Schedule of estimated useful life	'
	Asset Description	Estimated Useful Life
		(In Years)
	Manufacturing equipment		10
	Laboratory equipment		5
	Computer and office equipment		3
	Furniture and fixtures		7
	Software		3

Net_Loss_Per_Share_Tables

Net Loss Per Share (Tables)	12 Months Ended
	Dec. 31, 2013
Net Loss Per Share	'
Schedule of computation of basic and diluted net loss per share	'
	The following table sets forth the computation of basic and diluted net loss per share (in thousands, except per share amounts):
		Years Ended December 31,
		2013			2012			2011
	Numerator:
	Net loss	$	(272,812	)	$	(72,624	)	$	(64,852	)
	Denominator:
	Weighted average number of common shares used in net loss per share—basic and diluted		115,852			106,403			99,875
	Net loss per share—basic and diluted	$	(2.35	)	$	(0.68	)	$	(0.65	)
Schedule of potentially dilutive securities that have been excluded from computation of diluted weighted average shares outstanding	'
	The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding as they would be anti-dilutive (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Options to purchase common stock		20,928			19,540			16,425
	Shares subject to repurchase		—			80			160
			20,928			19,620			16,585

Collaboration_and_License_Agre1

Collaboration and License Agreements (Tables)	12 Months Ended
	Dec. 31, 2013
Collaboration and License Agreements	'
Schedule of amount recorded by the Company for share of net loss related to collaborative arrangement	'
	The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the years ended December 31, 2013 and 2012 (in thousands):
		Year Ended
		December 31,
		2013			2012
	Collaborative arrangements revenue(1)	$	2,914		$	—
	Collaboration expense		(42,074	)		(16,030	)
	Selling, general and administrative costs incurred by the Company(1)		(33,839	)		(5,092	)
	The Company's share of net loss	$	(72,999	)	$	(21,122	)
	-1
	Includes only collaborative arrangement revenue or selling, general and administrative costs attributable to the cost-sharing arrangement with Forest.

Fair_Value_of_Financial_Instru1

Fair Value of Financial Instruments (Tables)	12 Months Ended
	Dec. 31, 2013
Fair Value of Financial Instruments	'
Schedule of assets measured at fair value on a recurring basis	'
	The following tables present the assets the Company has measured at fair value on a recurring basis (in thousands):
				Fair Value Measurements at Reporting Date Using
	Description	December 31,		Quoted Prices in		Significant Other		Significant
		2013		Active Markets for		Observable		Unobservable
				Identical Assets		Inputs		Inputs
				(Level 1)		(Level 2)		(Level 3)
	Cash and cash equivalents:
	Money market funds	$	59,747	$	59,747	$	—	$	—
	U.S. government-sponsored securities		7,505		—		7,505		—
	Available-for-sale securities:
	U.S. Treasury securities		7,253		7,253		—		—
	U.S. government-sponsored securities		114,859		—		114,859		—
	Total	$	189,364	$	67,000	$	122,364	$	—
				Fair Value Measurements at Reporting Date Using
	Description	December 31,		Quoted Prices in		Significant Other		Significant
		2012		Active Markets for		Observable		Unobservable
				Identical Assets		Inputs		Inputs
				(Level 1)		(Level 2)		(Level 3)
	Cash and cash equivalents:
	Money market funds	$	111,368	$	111,368	$	—	$	—
	U.S. government-sponsored securities		2,500		—		2,500		—
	Available-for-sale securities:
	U.S. Treasury securities		15,052		15,052		—		—
	U.S. government-sponsored securities		16,476		—		16,476		—
	Total	$	145,396	$	126,420	$	18,976	$	—

AvailableforSale_Securities_Ta

Available-for-Sale Securities (Tables)	12 Months Ended
	Dec. 31, 2013
Available-for-Sale Securities	'
Schedule of summary of available-for-sale securities	'
	The following tables summarize the available-for-sale securities held at December 31, 2013 and 2012 (in thousands):
		Amortized Cost		Gross		Gross			Fair Value
				Unrealized		Unrealized
				Gains		Losses
	December 31, 2013:
	U.S. government-sponsored securities	$	114,857	$	6	$	(4	)	$	114,859
	U.S. Treasury securities		7,253		—		—			7,253
	Total	$	122,110	$	6	$	(4	)	$	122,112
		Amortized Cost		Gross		Gross			Fair Value
				Unrealized		Unrealized
				Gains		Losses
	December 31, 2012:
	U.S. government-sponsored securities	$	16,472	$	5	$	(1	)	$	16,476
	U.S. Treasury securities		15,051		1		—			15,052
	Total	$	31,523	$	6	$	(1	)	$	31,528

Inventory_Tables

Inventory (Tables)	12 Months Ended
	Dec. 31, 2013
Inventory	'
Schedule of Inventory	'
	Inventory consisted of the following (in thousands):
		December 31,
		2013		2012
	Raw materials	$	22,145	$	6,699

Property_and_Equipment_Tables

Property and Equipment (Tables)	12 Months Ended
	Dec. 31, 2013
Property and Equipment	'
Schedule of property and equipment	'
	Property and equipment, net consisted of the following (in thousands):
		December 31,
		2013			2012
	Manufacturing equipment	$	2,812		$	—
	Laboratory equipment		14,039			16,315
	Computer and office equipment		5,202			6,476
	Furniture and fixtures		2,365			2,449
	Software		12,352			11,047
	Construction in process		996			1,460
	Leased vehicles		4,472			—
	Leasehold improvements		36,827			36,770
			79,065			74,517
	Less accumulated depreciation and amortization		(41,689	)		(36,980	)
		$	37,376		$	37,537

Accrued_Expenses_Tables

Accrued Expenses (Tables)	12 Months Ended
	Dec. 31, 2013
Accrued Expenses	'
Schedule of accrued expenses	'
	Accrued expenses consisted of the following (in thousands):
		December 31,
		2013		2012
	Salaries and benefits	$	13,784	$	14,594
	Professional fees		531		1,031
	Accrued interest		856		—
	Other		3,267		5,546
		$	18,438	$	21,171

Notes_Payable_Tables

Notes Payable (Tables)	12 Months Ended
	Dec. 31, 2013
Notes Payable	'
Schedule of redemption price as percentage of outstanding principal balance	'
	Payment Dates	Redemption
		Percentage
	From and including January 1, 2014 to and including December 31, 2014		112	%
	From and including January 1, 2015 to and including December 31, 2015		105.5	%
	From and including January 1, 2016 to and including December 31, 2016		102.75	%
	From and including January 1, 2017 and thereafter		100	%

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2013
Commitments and Contingencies	'
Schedule of future minimum lease payments under all non-cancelable lease arrangements	'
	At December 31, 2013, future minimum lease payments under all non-cancelable lease arrangements were as follows (in thousands):
		Operating		Capital
		Leases		Leases
	2014	$	13,072	$	1,434
	2015		14,152		1,265
	2016		15,255		2,157
	2017		15,778		—
	2018		604		—
	Total future minimum lease payments	$	58,861		4,856
	Less amounts representing interest				(583	)
	Capital lease obligations at December 31, 2013				4,273
	Less current portion of capital lease obligations				(1,139	)
	Capital lease obligations, net of current portion			$	3,134

Stock_Benefit_Plans_Tables

Stock Benefit Plans (Tables)	12 Months Ended
	Dec. 31, 2013
Stock Benefit Plans	'
Summary of expense recognized for share-based compensation arrangements	'
	The following table summarizes the expense recognized for share-based compensation arrangements in the consolidated statements of operations (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Employee stock options	$	17,981		$	16,582		$	10,904
	Restricted stock awards		552			429			431
	Non-employee stock options		271			60			152
	Employee stock purchase plan		995			472			215
	Stock award		30			30			30
		$	19,829		$	17,573		$	11,732
Share-based compensation is reflected in the condensed consolidated statements of operations	'
	Share-based compensation is reflected in the consolidated statements of operations as follows for the years ended December 31, 2013, 2012 and 2011 (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Research and development	$	9,178		$	9,080		$	6,071
	Selling, general and administrative		10,651			8,493			5,661
		$	19,829		$	17,573		$	11,732
Summary of the unvested shares of restricted stock	'
		Shares			Weighted-Average
					Grant Date
					Fair Value
	Unvested at December 31, 2012		80,000		$	5.72
	Granted		8,333		$	14.94
	Vested		(88,333	)	$	6.59
	Forfeited		—		$	0
	Unvested at December 31, 2013		—		$	0
Schedule of weighted-average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model	'
		Years Ended December 31,
		2013			2012			2011
	Fair value of common stock	$	12.57		$	13.44		$	11.98
	Expected volatility		46.3	%		49.2	%		49.8	%
	Expected term (in years)		6.5			6.5			6.5
	Risk-free interest rate		1.6	%		1.2	%		2.4	%
	Expected dividend yield		—	%		—	%		—	%
Schedule of stock option activity under the share-based compensation plans, including performance-based options	'
		Shares of			Weighted-			Weighted-			Aggregate
		Common			Average			Average			Intrinsic
		Stock			Exercise			Contractual			Value
		Attributable			Price			Life
		to Options
								(in years)			(in thousands)
	Outstanding at December 31, 2012		19,539,429		$	7.75			6.33		$	79,140
	Granted		3,857,370		$	12.57
	Exercised		(1,823,141	)	$	3.37
	Cancelled		(645,784	)	$	12.5
	Outstanding at December 31, 2013		20,927,874		$	8.87			6.14		$	71,616
	Vested or expected to vest at December 31, 2013		19,873,836		$	8.82			6.07		$	68,903
	Exercisable at December 31, 2013(1)		11,537,396		$	6.89			4.77		$	59,014
	-1
	All stock options granted under the 2002 Equity Plan and the 2005 Equity Plan contain provisions allowing for the early exercise of such options into restricted stock. The exercisable shares disclosed above represent those that were vested as of December 31, 2013.

Income_Taxes_Tables

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2013
Income Taxes	'
Reconciliation of income taxes from continuing operations computed using U.S. federal statutory rate to that reflected in operations	'
	A reconciliation of income taxes computed using the U.S. federal statutory rate to that reflected in operations follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Income tax benefit using U.S. federal statutory rate	$	(92,756	)	$	(24,692	)	$	(22,050	)
	Permanent differences		1,413			288			245
	State income taxes, net of federal benefit		(13,684	)		(3,835	)		(3,531	)
	Stock compensation		3,830			3,531			2,104
	Tax credits		(5,089	)		(10,420	)		509
	Expiring net operating losses and tax credits		—			564			803
	Effect of change in state tax rate on deferred tax assets and deferred tax liabilities		1,057			—			98
	Change in the valuation allowance		105,186			34,577			20,955
	Other		43			(13	)		870
		$	—		$	—		$	3
Schedule of components of deferred tax assets and liabilities	'
	Components of the Company's deferred tax assets and liabilities are as follows (in thousands):
		December 31,
		2013			2012
	Deferred tax assets:
	Net operating loss carryforwards	$	231,660		$	127,928
	Tax credit carryforwards		29,533			24,444
	Capitalized research and development		11,939			17,305
	Deferred revenue		6,433			8,300
	Other		29,223			25,036
	Total deferred tax assets		308,788			203,013
	Valuation allowance		(308,788	)		(203,013	)
	Net deferred tax asset	$	—		$	—

Selected_Quarterly_Financial_D1

Selected Quarterly Financial Data (Unaudited) (Tables)	12 Months Ended
	Dec. 31, 2013
Selected Quarterly Financial Data (Unaudited)	'
Schedule of quarterly financial information	'
		First			Second			Third			Fourth			Total
		Quarter			Quarter			Quarter			Quarter			Year
		(in thousands, except per share data)
	2013
	Collaborative arrangements revenue	$	3,255		$	9,663		$	4,932		$	5,031		$	22,881
	Total cost and expenses		92,088			69,543			61,483			51,769			274,883
	Other income (expense), net		(5,069	)		(5,269	)		(5,224	)		(5,248	)		(20,810	)
	Net loss		(93,902	)		(65,149	)		(61,775	)		(51,986	)		(272,812	)
	Net loss per share—basic and diluted	$	(0.87	)	$	(0.57	)	$	(0.51	)	$	(0.43	)	$	(2.35	)
		First			Second			Third			Fourth			Total
		Quarter			Quarter			Quarter			Quarter			Year
		(in thousands, except per share data)
	2012
	Collaborative arrangements revenue	$	12,248		$	14,604		$	96,413		$	26,980		$	150,245
	Total cost and expenses		47,884			55,438			48,805			70,880			223,007
	Other income (expense), net		35			31			27			45			138
	Net income (loss)		(35,601	)		(40,803	)		47,635			(43,855	)		(72,624	)
	Basic net income (loss) per share	$	(0.34	)	$	(0.38	)	$	0.44		$	(0.41	)	$	(0.68	)
	Diluted net income (loss) per share	$	(0.34	)	$	(0.38	)	$	0.42		$	(0.41	)	$	(0.68	)

Nature_of_Business_Details

Nature of Business (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Nature of Business	'	'
Accumulated deficit since inception	$777,828	$505,016

Summary_of_Significant_Account3

Summary of Significant Accounting Policies (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash and Cash Equivalents	'	'	'
Cash Equivalent included in cash and cash equivalent	$67,300,000	$113,900,000	'
Restricted Cash	'	'	'
Restricted cash securing letters of credit	8,147,000	7,647,000	'
Available-for-Sale Securities	'	'	'
Minimum original maturity period of entity's short-term investments in order to classify them as available for sale	'3 months	'	'
Other-than-temporary impairments	0	0	0
Letters of credit	'	'	'
Restricted Cash	'	'	'
Contingent liability under unused letters of credit	8,100,000	7,600,000	'
Restricted cash securing letters of credit	$8,100,000	$7,600,000	'

Summary_of_Significant_Account4

Summary of Significant Accounting Policies (Details 2) (USD $)

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

In Thousands, unless otherwise specified

Forest Laboratories, Inc.

AstraZeneca

Supplier concentration

Accounts receivable

Accounts receivable

Accounts receivable

Accounts receivable

Revenue

Revenue

Revenue

Revenue

Revenue

Revenue

Revenue

Revenue

Revenue

Revenue

Revenue

item

item

Accounts receivable balances

Accounts receivable balances

Accounts receivable balances

Accounts receivable balances

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

AstraZeneca

AstraZeneca

Forest Laboratories, Inc.

Almirall, S.A.

Astellas Pharma Inc.

Astellas Pharma Inc.

Revenue and accounts receivable by major customer; third-party manufacturers

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of third-party manufacturers

'

'

'

'

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of manufacturing facilities

'

'

'

'

3

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Revenue and accounts receivable by major customer (as a percent)

'

'

'

'

'

84.00%

69.00%

16.00%

31.00%

13.00%

67.00%

64.00%

57.00%

14.00%

31.00%

25.00%

3.00%

5.00%

5.00%

16.00%

Accounts receivable

$513

$457

'

$0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of collaboration agreements

'

'

'

1

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Net Profit or Net Loss Sharing

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of the pre-tax net profit or loss

'

'

50.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Summary_of_Significant_Account5

Summary of Significant Accounting Policies (Details 3) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Additional Disclosure for Income Statement	'	'	'
Selling, general, and administrative expense	$123,228	$92,538	$45,920
Patents	'	'	'
Additional Disclosure for Income Statement	'	'	'
Selling, general, and administrative expense	$3,200	$3,500	$2,200

Summary_of_Significant_Account6

Summary of Significant Accounting Policies (Details 4) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
	segment
Segment Information	'	'
Number of reportable segments	1	'
Significant impairment of long-lived assets	$0	$0
Manufacturing equipment	'	'
Property and equipment	'	'
Estimated useful life	'10 years	'
Laboratory equipment	'	'
Property and equipment	'	'
Estimated useful life	'5 years	'
Computer and office equipment	'	'
Property and equipment	'	'
Estimated useful life	'3 years	'
Furniture and fixtures	'	'
Property and equipment	'	'
Estimated useful life	'7 years	'
Software	'	'
Property and equipment	'	'
Estimated useful life	'3 years	'

Net_Loss_Per_Share_Details

Net Loss Per Share (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Numerator:	'	'	'	'	'	'	'	'	'	'	'
Net loss	($51,986)	($61,775)	($65,149)	($93,902)	($43,855)	$47,635	($40,803)	($35,601)	($272,812)	($72,624)	($64,852)
Denominator:	'	'	'	'	'	'	'	'	'	'	'
Weighted average number of common shares used in net loss per share - basic and diluted (in shares)	'	'	'	'	'	'	'	'	115,852	106,403	99,875
Net loss per share - basic and diluted (in dollars per share)	'	'	'	'	'	'	'	'	($2.35)	($0.68)	($0.65)

Net_Loss_Per_Share_Details_2

Net Loss Per Share (Details 2)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Potentially dilutive securities	'	'	'
Dilutive securities excluded from the computation of diluted weighted average shares outstanding	20,928	19,620	16,585
Options to purchase common stock	'	'	'
Potentially dilutive securities	'	'	'
Dilutive securities excluded from the computation of diluted weighted average shares outstanding	20,928	19,540	16,425
Shares subject to repurchase	'	'	'
Potentially dilutive securities	'	'	'
Dilutive securities excluded from the computation of diluted weighted average shares outstanding	'	80	160

Collaboration_and_License_Agre2

Collaboration and License Agreements (Details) (USD $)

3 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2012

Mar. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Sep. 30, 2007

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Sep. 30, 2009

Dec. 31, 2013

Sep. 30, 2012

Aug. 31, 2012

Oct. 31, 2011

Jul. 31, 2009

Sep. 30, 2008

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Convertible preferred stock

Development and sales milestones

Development milestones

Development milestones

Development milestones

Development milestones

Development milestones

Development milestones

Commercialization milestone

Maximum

item

item

item

item

Sales milestones

Collaboration and License Agreements

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Up-front fee received

'

'

'

'

'

'

'

'

'

'

'

$70,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

Cumulative license fees and development milestone payments received

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

205,000,000

'

'

Equity investment in the entity's capital stock

'

'

'

'

'

'

'

'

'

'

'

'

25,000,000

'

'

'

'

'

'

'

'

'

'

'

'

Milestone payment to be received by company upon milestone achievement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

100,000,000

Asset value for contingent equity investment by collaborative party recorded at inception of agreement

'

'

'

'

'

'

'

'

'

'

'

9,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

Incremental deferred revenue related to contingent equity investment

'

'

'

'

'

'

'

'

'

'

'

9,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

Collaboration expense

'

'

'

'

'

'

'

'

-42,074,000

-16,030,000

'

'

-42,074,000

-16,030,000

'

'

'

'

'

'

'

'

'

'

'

Selling, general and administrative costs incurred by the Company

'

'

'

'

'

'

'

'

'

'

'

'

-33,839,000

-5,092,000

'

'

'

'

'

'

'

'

'

'

'

The Company's share of net loss

'

'

'

'

'

'

'

'

'

'

'

'

-72,999,000

-21,122,000

'

'

'

'

'

'

'

'

'

'

'

Issuance of Convertible preferred stock (in shares)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,083,333

'

'

'

'

'

'

'

'

'

Number of milestones achieved under collaboration agreement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2

2

'

'

6

'

'

Milestone payment received

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

85,000,000

'

20,000,000

20,000,000

10,000,000

'

'

'

Number of milestone payments recognized

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4

'

'

'

'

'

'

'

'

Collaborative arrangements revenue

5,031,000

4,932,000

9,663,000

3,255,000

26,980,000

96,413,000

14,604,000

12,248,000

22,881,000

150,245,000

65,871,000

'

2,914,000

'

'

'

'

'

'

'

'

'

'

'

'

Collaborative arangements revenue recognized

'

'

'

'

'

'

'

'

'

'

'

'

'

100,400,000

41,800,000

'

'

'

'

'

'

'

'

'

'

Net cost sharing offset or incremental expense related to research and development expense

'

'

'

'

'

'

'

'

'

'

'

'

($2,200,000)

($2,100,000)

$7,900,000

'

'

'

'

'

'

'

'

'

'

Percentage of net profit from commercialization

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

'

Percentage of net loss from commercialization

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

'

Collaboration_and_License_Agre3

Collaboration and License Agreements (Details 2) (USD $)

3 Months Ended

12 Months Ended

1 Months Ended

3 Months Ended

12 Months Ended

1 Months Ended

3 Months Ended

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2012

Mar. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

31-May-09

Apr. 30, 2009

Jun. 30, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

31-May-13

Nov. 30, 2009

Apr. 30, 2009

Nov. 30, 2010

Apr. 30, 2009

Jun. 30, 2013

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

item

item

Convertible preferred stock

Development and sales milestones

Development milestones

Development milestones

Amended Development Milestones

Convertible preferred stock

item

Collaboration and License Agreements

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Up-front fee received, net

'

'

'

'

'

'

'

'

'

'

'

$38,000,000

'

'

'

'

'

'

'

'

'

'

'

Up-front fee received

'

'

'

'

'

'

'

'

'

'

'

40,000,000

'

'

'

'

'

'

'

'

'

'

'

Equity investment in the entity's capital stock

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15,000,000

'

'

'

'

Contingent equity investment to be received form forward purchase contract

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15,000,000

'

Asset value for contingent equity investment by collaborative party recorded at inception of agreement

'

'

'

'

'

'

'

'

'

'

'

'

6,000,000

'

'

'

'

'

'

'

'

'

'

Incremental deferred revenue related to contingent equity investment

'

'

'

'

'

'

'

'

'

'

'

'

6,000,000

'

'

'

'

'

'

'

'

'

'

Issuance of Convertible preferred stock (in shares)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

681,819

'

'

'

'

Maximum contingent equity and milestone payments to be received

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

40,000,000

'

'

'

Number of milestones achieved under collaboration agreement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2

Milestone payment received

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

20,000,000

'

'

Revenue recognized from sale of API

'

'

'

'

'

'

'

'

'

'

'

'

'

'

11,100,000

3,500,000

500,000

'

'

'

'

'

'

Revenue recognized in royalty payments

'

'

'

'

'

'

'

'

'

'

'

'

'

'

200,000

'

'

'

'

'

'

'

'

Revenue recognized in commercial launch milestones

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,900,000

'

'

'

'

'

'

'

'

Collaborative arrangements revenue

5,031,000

4,932,000

9,663,000

3,255,000

26,980,000

96,413,000

14,604,000

12,248,000

22,881,000

150,245,000

65,871,000

'

'

'

13,100,000

21,200,000

20,600,000

'

'

'

'

'

'

Milestone payment received, net of foreign withholding taxes

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

19,000,000

'

1,900,000

Milestones, net of foreign tax withholdings

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,000,000

Total milestone payment due upon the first commercial launch in all major European Union countries

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

17,000,000

Number of major European Union countries

'

'

'

'

'

'

'

'

'

'

'

'

'

5

5

'

'

'

'

'

'

'

'

Number of major European Union countries in which commercial launch occurred

'

'

'

'

'

'

'

'

'

'

'

'

'

2

'

'

'

'

'

'

'

'

'

Milestone payment due upon the first commercial launch in each of the five major European Union countries

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$4,000,000

'

'

'

'

'

Collaboration_and_License_Agre4

Collaboration and License Agreements (Details 3) (USD $)

3 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2012

Mar. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Mar. 31, 2013

Nov. 30, 2009

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Astellas Pharma Inc.

Additional development milestones

Phase 3 milestones

Japanese NDA equivalent filing milestone

Approval of Japanese NDA equivalent filing milestone

Maximum

Collaboration and License Agreements

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Up-front fee received

'

'

'

'

'

'

'

'

'

'

'

'

$30,000,000

'

'

'

'

'

'

'

Milestone payment to be received by company upon milestone achievement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15,000,000

15,000,000

15,000,000

Estimated development period prior to assessment

'

'

'

'

'

'

'

'

'

'

'

'115 months

'

'

'

'

'

'

'

'

Estimated development period

'

'

'

'

'

'

'

'

'

'

'

'85 months

'

'

'

'

'

'

'

'

Revenue recognized as a result of revised estimate of development period

'

'

'

'

'

'

'

'

'

'

'

'

'

1,500,000

'

'

'

'

'

'

Up-front license fee deferred

'

'

'

'

'

'

'

'

'

'

'

'

'

16,500,000

'

'

'

'

'

'

Collaborative arrangements revenue

5,031,000

4,932,000

9,663,000

3,255,000

26,980,000

96,413,000

14,604,000

12,248,000

22,881,000

150,245,000

65,871,000

'

'

5,800,000

3,900,000

3,500,000

'

'

'

'

Revenue recognized from sale of API

'

'

'

'

'

'

'

'

'

'

'

'

'

1,200,000

800,000

400,000

'

'

'

'

Total milestone payments to be received

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$45,000,000

'

'

'

Collaboration_and_License_Agre5

Collaboration and License Agreements (Details 4) (AstraZeneca, USD $)	1 Months Ended	12 Months Ended
	Oct. 31, 2012	Dec. 31, 2013
Collaboration and License Agreements	'	'
Prior notice period to terminate the agreement	'180 days	'
Up-front fee received	$25,000,000	'
Estimated development period	'	'44 months
Total amount of non-contingent arrangement consideration	26,900,000	'
Amount of arrangement consideration for clinical trial material supply services and research, development and regulatory activities	1,900,000	'
Discount rate utilized in analysis (as a percent)	11.50%	'
Arrangement Consideration allocated to the License Deliverable	24,700,000	'
Arrangement Consideration allocated to the R&D Services	300,000	'
Arrangement Consideration allocated to the JDC services	28,000	'
Arrangement Consideration allocated to the clinical trial material supply services	100,000	'
Arrangement Consideration allocated to Co-Promotion Deliverable	1,800,000	'
Remaining Arrangement Consideration received and allocated to the remaining deliverables, which was deferred	300,000	'
Percentage of costs of clinical trial material supply services and research, development and regulatory activities allocated	55.00%	'
Net cost sharing offset or incremental expense related to research and development expense	'	-1,900,000
Collaborative arrangements revenue earned	'	1,000,000
Sales milestones	'	'
Collaboration and License Agreements	'	'
Milestone payment to be received by company upon milestone achievement	$125,000,000	'
Commercialization milestone	'	'
Collaboration and License Agreements	'	'
Percentage of net profit from commercialization	55.00%	'
Percentage of net loss from commercialization	55.00%	'

Collaboration_and_License_Agre6

Collaboration and License Agreements (Details 5) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Collaboration and License Agreements	'	'	'
Research and development expense	$102,378,000	$113,474,000	$86,093,000
Other Collaboration and License Agreements	'	'	'
Collaboration and License Agreements	'	'	'
Aggregate up-front fee paid	5,800,000	'	'
Contingent milestone payable per product, maximum	114,500,000	'	'
Research and development expense	3,600,000	8,200,000	6,000,000
Other Collaboration and License Agreements | Sales milestones	'	'	'
Collaboration and License Agreements	'	'	'
Contingent milestone payable per product	35,000,000	'	'
Other Collaboration and License Agreements | Development milestones	'	'	'
Collaboration and License Agreements	'	'	'
Contingent milestone payable	99,500,000	'	'
Milestone payment	1,000,000	'	'
Contingent milestone payable per product	21,500,000	'	'
Other Collaboration and License Agreements | Regulatory milestones	'	'	'
Collaboration and License Agreements	'	'	'
Contingent milestone payable	265,500,000	'	'
Milestone payment	0	'	'
Contingent milestone payable per product	$58,000,000	'	'

Fair_Value_of_Financial_Instru2

Fair Value of Financial Instruments (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Description	'	'
Available-for-sale securities	$122,112	$31,528
Transfers between Level 1 and Level 2 of the fair value hierarchy	0	0
Recurring basis | Fair Value	'	'
Description	'	'
Total assets fair value	189,364	145,396
Recurring basis | Fair Value | Money market funds	'	'
Description	'	'
Cash and cash equivalents	59,747	111,368
Recurring basis | Fair Value | U.S. Treasury securities	'	'
Description	'	'
Available-for-sale securities	7,253	15,052
Recurring basis | Fair Value | U.S. government-sponsored securities	'	'
Description	'	'
Cash and cash equivalents	7,505	2,500
Available-for-sale securities	114,859	16,476
Recurring basis | Quoted Prices in Active Markets for Identical Assets (Level 1)	'	'
Description	'	'
Total assets fair value	67,000	126,420
Recurring basis | Quoted Prices in Active Markets for Identical Assets (Level 1) | Money market funds	'	'
Description	'	'
Cash and cash equivalents	59,747	111,368
Recurring basis | Quoted Prices in Active Markets for Identical Assets (Level 1) | U.S. Treasury securities	'	'
Description	'	'
Available-for-sale securities	7,253	15,052
Recurring basis | Significant Other Observable Inputs (Level 2)	'	'
Description	'	'
Total assets fair value	122,364	18,976
Recurring basis | Significant Other Observable Inputs (Level 2) | U.S. government-sponsored securities	'	'
Description	'	'
Cash and cash equivalents	7,505	2,500
Available-for-sale securities	$114,859	$16,476

AvailableforSale_Securities_De

Available-for-Sale Securities (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
	item	item
Available-for-Sale Securities	'	'	'
Amortized Cost	$122,110,000	$31,523,000	'
Gross Unrealized Gains	6,000	6,000	'
Gross Unrealized Losses	-4,000	-1,000	'
Fair Value	122,112,000	31,528,000	'
Contractual maturity period, maximum	'1 year	'	'
Number of investments classified as available-for-sale securities in an unrealized loss position	12	3	'
Number of investments classified as available-for-sale securities in an unrealized loss position for more than twelve months	0	0	'
Aggregate fair value of securities none of which had been in an unrealized loss position for more than twelve months	38,700,000	3,000,000	'
Proceeds from maturities of available-for-sale securities	'	89,800,000	212,300,000
Proceeds from sales of available-for-sale securities	0	51,000,000	10,000,000
U.S. government-sponsored securities	'	'	'
Available-for-Sale Securities	'	'	'
Amortized Cost	114,857,000	16,472,000	'
Gross Unrealized Gains	6,000	5,000	'
Gross Unrealized Losses	-4,000	-1,000	'
Fair Value	114,859,000	16,476,000	'
U.S. Treasury securities	'	'	'
Available-for-Sale Securities	'	'	'
Amortized Cost	7,253,000	15,051,000	'
Gross Unrealized Gains	'	1,000	'
Fair Value	$7,253,000	$15,052,000	'

Inventory_Details

Inventory (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Inventory	'	'
Raw materials	$22,145	$6,699

Property_and_Equipment_Details

Property and Equipment (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Property and equipment	'	'	'
Property and equipment, gross	$79,065,000	$74,517,000	'
Less accumulated depreciation and amortization	-41,689,000	-36,980,000	'
Property and equipment, net	37,376,000	37,537,000	'
Depreciation and amortization expense	11,729,000	11,325,000	9,999,000
Assets under capital lease	5,500,000	1,400,000	'
Accumulated amortization balances related to assets under capital lease	1,200,000	900,000	'
301 Binney Street, Cambridge, Massachusetts	'	'	'
Property and equipment	'	'	'
Additional term of the lease	'24 months	'	'
Manufacturing equipment	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	2,812,000	'	'
Laboratory equipment	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	14,039,000	16,315,000	'
Computer and office equipment	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	5,202,000	6,476,000	'
Furniture and fixtures	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	2,365,000	2,449,000	'
Software	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	12,352,000	11,047,000	'
Construction in process	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	996,000	1,460,000	'
Leased vehicles	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	4,472,000	'	'
Leasehold improvements	'	'	'
Property and equipment	'	'	'
Property and equipment, gross	$36,827,000	$36,770,000	'

Accrued_Expenses_Details

Accrued Expenses (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Accrued Expenses	'	'
Salaries and benefits	$13,784	$14,594
Professional fees	531	1,031
Accrued interest	856	'
Other	3,267	5,546
Total accrued expense	$18,438	$21,171

Notes_Payable_Details

Notes Payable (Details) (USD $)	12 Months Ended		0 Months Ended	12 Months Ended
	Dec. 31, 2013	Jan. 31, 2013	Jan. 04, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013
			Notes Payable	Notes Payable	Notes Payable	Notes Payable	Notes Payable	Notes Payable
					From and including January 1, 2014 to and including December 31, 2014	From and including January 1, 2015 to and including December 31, 2015	From and including January 1, 2016 to and including December 31, 2016	From and including January 1, 2017 and thereafter
Notes Payable	'	'	'	'	'	'	'	'
Payment start date	'	'	'	'	1-Jan-14	1-Jan-15	1-Jan-16	1-Jan-17
Payment end date	'	'	'	'	31-Dec-14	31-Dec-15	31-Dec-16	'
Aggregate principal amount of notes issued in private placement	'	'	$175,000,000	'	'	'	'	'
Annual interest rate of notes (as a percent)	'	11.00%	11.00%	'	'	'	'	'
Percentage of net sales of LINZESS considered to determine quarterly payments on the notes	'	'	'	7.50%	'	'	'	'
Margin over U.S. Treasury Rate (as a percent)	'	'	'	1.00%	'	'	'	'
Redemption Percentage	'	'	'	'	112.00%	105.50%	102.75%	100.00%
Upfront cash proceeds	175,000,000	'	175,000,000	'	'	'	'	'
Discount on issuance of debt	'	'	400,000	'	'	'	'	'
Debt issuance costs capitalized	'	'	7,300,000	'	'	'	'	'
Estimated fair value	'	'	'	$183,800,000	'	'	'	'

Commitments_and_Contingencies_1

Commitments and Contingencies (Details) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013
Commitments and Contingencies	'
Reimbursement for financing capital improvements	$17.50
Minimum purchase requirement and other firm commitments related to supply contracts by year	'
2014	8.7
2015	5.9
2016	7.9
2017	7.9
2018	2.5
2019 and thereafter	5
Office and laboratory space in Cambridge, Massachusetts	'
Commitments and Contingencies	'
Letter of credit outstanding amount	$7.60
Rentable area leased (in square feet)	70,000

Commitments_and_Contingencies_2

Commitments and Contingencies (Details 2) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013
Vehicle fleet	'
Capital lease obligation	'
Initial term of the lease	'36 months
Weighted average interest rate on the outstanding capital lease obligations (as a percent)	7.70%
Letters of credit securing capital lease obligations	$0.50
Computer and office equipment	'
Capital lease obligation	'
Weighted average interest rate on the outstanding capital lease obligations (as a percent)	8.00%

Commitments_and_Contingencies_3

Commitments and Contingencies (Details 3) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Future minimum lease payments under operating leases	'	'	'
2014	$13,072,000	'	'
2015	14,152,000	'	'
2016	15,255,000	'	'
2017	15,778,000	'	'
2018	604,000	'	'
Total future minimum lease payments	58,861,000	'	'
Future minimum lease payments under capital leases	'	'	'
2014	1,434,000	'	'
2015	1,265,000	'	'
2016	2,157,000	'	'
Total future minimum lease payments	4,856,000	'	'
Less amounts representing interest	-583,000	'	'
Capital lease obligations at the end of the period	4,273,000	'	'
Less current portion of capital lease obligations	1,139,000	261,000	'
Capital lease obligations, net of current portion	3,134,000	308,000	'
Continuing operations	'	'	'
Operating lease	'	'	'
Rent expense	$8,800,000	$7,200,000	$6,600,000

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)	12 Months Ended		1 Months Ended	3 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Feb. 29, 2012	Jun. 30, 2013	Dec. 31, 2013	Dec. 31, 2013
	item		Class A common stock	Class A common stock	Class A common stock	Class B common stock
Stockholders' Equity	'	'	'	'	'	'
Number of series of common stock designated	2	'	'	'	'	'
Number of voting rights per share	'	'	'	'	1	1
Number of voting rights per share if the matter is an adoption agreement of merger or consolidation, an adoption of a resolution with respect to sale, lease, or exchange of the Company's assets or an adoption of dissolution or liquidation of the Company	'	'	'	'	'	10
Number of voting rights per share if any individual, entity, or group seeks to obtain or has obtained beneficial ownership of 30% or more of the Company's outstanding shares of common stock	'	'	'	'	'	10
Minimum percentage of beneficial ownership in entity's outstanding shares of common stock used to determine number of voting rights allowed per share of common stock	30.00%	'	'	'	'	'
Number of shares of Class A common stock to be received for each share of Class B common stock converted	1	'	'	'	'	'
Threshold number of shares of Class B common stock outstanding used to determine date of conversion	19,561,556	'	'	'	'	'
Percentage of the number of shares of Class B common stock outstanding immediately following the completion of an initial public offering used to determine date of conversion	25.00%	'	'	'	'	'
Shares sold	'	'	6,037,500	11,204,948	'	'
Issuance price per share (in dollars per share)	'	'	$15.09	$13	'	'
Proceeds from issuance of common stock	$137,766	$85,228	$85,200	$137,800	'	'

Stock_Benefit_Plans_Details

Stock Benefit Plans (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Restricted Stock	'	'	'
Expense recognized for share-based compensation arrangements	$19,829	$17,573	$11,732
Employee stock options	'	'	'
Restricted Stock	'	'	'
Expense recognized for share-based compensation arrangements	17,981	16,582	10,904
Restricted stock awards	'	'	'
Restricted Stock	'	'	'
Expense recognized for share-based compensation arrangements	552	429	431
Non-employee stock options	'	'	'
Restricted Stock	'	'	'
Expense recognized for share-based compensation arrangements	271	60	152
Employee stock purchase plan	'	'	'
Restricted Stock	'	'	'
Expense recognized for share-based compensation arrangements	995	472	215
Stock awards	'	'	'
Restricted Stock	'	'	'
Expense recognized for share-based compensation arrangements	$30	$30	$30

Stock_Benefit_Plans_Details_2

Stock Benefit Plans (Details 2) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Share-based compensation is reflected in the condensed consolidated statements of operations	'	'	'
Share-based compensation	$19,829	$17,573	$11,732
Research and development	'	'	'
Share-based compensation is reflected in the condensed consolidated statements of operations	'	'	'
Share-based compensation	9,178	9,080	6,071
Selling, general and administrative	'	'	'
Share-based compensation is reflected in the condensed consolidated statements of operations	'	'	'
Share-based compensation	$10,651	$8,493	$5,661

Stock_Benefit_Plans_Details_3

Stock Benefit Plans (Details 3) (USD $)

12 Months Ended

0 Months Ended

12 Months Ended

12 Months Ended

12 Months Ended

12 Months Ended

12 Months Ended

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Mar. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2009

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2010

Dec. 31, 2013

Dec. 31, 2010

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2009

item

Restricted Stock

Restricted Stock

Restricted Stock

Restricted Stock

Restricted Stock

Options to purchase common stock

Options to purchase common stock

Options to purchase common stock

Options to purchase common stock

Options to purchase common stock

Performance-based milestone options

Performance-based milestone options

Performance-based milestone options

The Plans

The Plans

The Plans

The Plans

The Plans

The Plans

2010 Plan

2010 Plan

2010 Purchase Plan

2010 Purchase Plan

2010 Purchase Plan

2005 Equity Plan

2002 Equity Plan

2005 Equity Plan and director compensation program

2005 Equity Plan and director compensation program

Class A common stock

Class B common stock

Time-accelerated stock options

Time-accelerated stock options

Time-accelerated stock options

Time-accelerated stock options

Time-accelerated stock options

Class A common stock

Restricted Stock

Restricted Stock

Minimum

Maximum

Restricted Stock

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of share-based compensation plans pursuant to which awards are currently being made

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of share-based compensation plans under which there are outstanding awards

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares reserved for issuance

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

6,000,000

'

400,000

'

'

'

'

'

Threshold number of additional shares available for future grant

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

6,600,000

'

1,000,000

'

'

'

'

'

'

Percentage for the threshold number of additional shares available for future grant, expressed as percentage of common stock outstanding on the last day of the immediately preceding fiscal year

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4.00%

'

'

'

1.00%

'

'

'

'

Shares available for future grant

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

7,868,767

'

'

'

'

'

7,263,256

'

574,658

'

'

30,853

0

'

'

Purchase price as a percentage of fair market value of a share of common stock on the first or last day of an offering period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

85.00%

'

'

'

'

'

Offering period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'6 months

'

'

'

'

'

Expiration period

'

'

'

'

'

'

'

'

'10 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Vesting period

'

'

'

'

'4 years

'

'

'

'4 years

'

'

'

'

'

'

'

'

'

'

'

'6 years

'10 years

'

'

'

'

'

'

'

'

'

Summary of unvested shares of restricted stock, shares

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Outstanding at the beginning of the period ( in shares)

'

'

'

'

80,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Granted (in shares)

'

'

'

'

8,333

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

8,333

515,549

Vested (in shares)

'

'

'

833

-88,333

'

'

115,549

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Outstanding at the end of the period (in shares)

'

'

'

'

'

80,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Summary of unvested shares of restricted stock, weighted-average grant date fair value

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Outstanding at the beginning of the period (in dollars per share)

'

'

'

'

$5.72

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Granted (in dollars per share)

'

'

'

'

$14.94

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Vested (in dollars per share)

'

'

'

'

$6.59

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Forfeited (in dollars per share)

'

'

'

'

$0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Outstanding at the end of the period (in dollars per share)

'

'

'

'

$0

$5.72

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Weighted-average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Fair value of common stock (in dollars per share)

'

'

'

'

'

'

'

'

$12.57

$13.44

$11.98

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Expected volatility (as a percent)

'

'

'

'

'

'

'

'

46.30%

49.20%

49.80%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Expected term

'

'

'

'

'

'

'

'

'6 years 6 months

'6 years 6 months

'6 years 6 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Risk-free interest rate (as a percent)

'

'

'

'

'

'

'

'

1.60%

1.20%

2.40%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Additional disclosures

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Option exercisable (in shares)

'

'

'

'

'

'

'

'

11,537,396

'

'

13,009,834

7,918,040

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares vested as a result of milestone or service period achievements

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

253,334

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares issuable under outstanding options

'

'

'

'

'

80,000

'

'

20,927,874

19,539,429

'

'

'

'

'

'

'

570,000

823,334

'

'

'

'

'

'

'

'

'

'

'

'

Share-based compensation

$19,829,000

$17,573,000

$11,732,000

'

$552,000

$429,000

$431,000

'

'

'

'

'

'

$100,000

$1,000,000

$500,000

'

'

$500,000

$800,000

'

$100,000

'

'

'

'

'

'

'

'

'

Unrecognized share-based compensation

'

'

'

'

$0

'

'

'

$34,800,000

'

'

'

'

$3,900,000

'

'

'

$200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

Vested (in shares)

'

'

'

'

'

'

'

'

19,873,836

'

'

'

'

15,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock_Benefit_Plans_Details_4

Stock Benefit Plans (Details 4) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Stock options	'	'	'
Shares of Common Stock Attributable to Options	'	'	'
Outstanding at the beginning of the period (in shares)	19,539,429	'	'
Granted (in shares)	3,857,370	'	'
Exercised (in shares)	-1,823,141	'	'
Cancelled (in shares)	-645,784	'	'
Outstanding at the end of the period (in shares)	20,927,874	19,539,429	'
Vested or expected to vest at the end of the period (in shares)	19,873,836	'	'
Exercisable at the end of the period (in shares)	11,537,396	'	'
Weighted-Average Exercise Price	'	'	'
Outstanding at the beginning of the period (in dollars per share)	$7.75	'	'
Granted (in dollars per share)	$12.57	'	'
Exercised (in dollars per share)	$3.37	'	'
Cancelled (in dollars per share)	$12.50	'	'
Outstanding at the end of the period (in dollars per share)	$8.87	$7.75	'
Vested or expected to vest at the end of the period (in dollars per share)	$8.82	'	'
Exercisable at the end of the period (in dollars per share)	$6.89	'	'
Weighted-Average Contractual Life	'	'	'
Outstanding at the beginning of the period	'6 years 1 month 20 days	'6 years 3 months 29 days	'
Outstanding at the end of the period	'6 years 1 month 20 days	'6 years 3 months 29 days	'
Vested or expected to vest at the end of the period	'6 years 25 days	'	'
Exercisable at the end of the period	'4 years 9 months 7 days	'	'
Aggregate Intrinsic Value	'	'	'
Outstanding at the beginning of the period	$79,140,000	'	'
Outstanding at the end of the period	71,616,000	79,140,000	'
Vested or expected to vest at the end of the period	68,903,000	'	'
Exercisable at the end of the period	59,014,000	'	'
Weighted average grant date fair value (in dollars per share)	$5.96	$6.62	$6.21
Total intrinsic value of options exercised	19,700,000	8,600,000	17,400,000
Unrecognized share-based compensation	'	'	'
Unrecognized share-based compensation	34,800,000	'	'
Weighted average period for recognition	'2 years 9 months 11 days	'	'
Restricted Stock	'	'	'
Shares of Common Stock Attributable to Options	'	'	'
Outstanding at the end of the period (in shares)	'	80,000	'
Weighted-Average Exercise Price	'	'	'
Outstanding at the end of the period (in dollars per share)	'	$5.72	'
Unrecognized share-based compensation	'	'	'
Unrecognized share-based compensation	$0	'	'

Income_Taxes_Details

Income Taxes (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Taxes	'	'	'
Provision for state taxes	'	'	$3,000
Reconciliation of income taxes	'	'	'
Income tax benefit using U.S. federal statutory rate	-92,756,000	-24,692,000	-22,050,000
Permanent differences	1,413,000	288,000	245,000
State income taxes, net of federal benefit	-13,684,000	-3,835,000	-3,531,000
Stock compensation	3,830,000	3,531,000	2,104,000
Tax credits	-5,089,000	-10,420,000	509,000
Expiring net operating losses and tax credits	'	564,000	803,000
Effect of change in state tax rate on deferred tax assets and deferred tax liabilities	1,057,000	'	98,000
Change in the valuation allowance	105,186,000	34,577,000	20,955,000
Other	43,000	-13,000	870,000
Benefit for income taxes from continuing operations	'	'	3,000
Deferred tax assets:	'	'	'
Net operating loss carryforwards	231,660,000	127,928,000	'
Tax credit carryforwards	29,533,000	24,444,000	'
Capitalized research and development	11,939,000	17,305,000	'
Deferred revenue	6,433,000	8,300,000	'
Other	29,223,000	25,036,000	'
Total deferred tax assets	308,788,000	203,013,000	'
Valuation allowance	-308,788,000	-203,013,000	'
Increase in valuation allowance	$105,800,000	$34,800,000	'

Income_Taxes_Details_2

Income Taxes (Details 2) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Millions, unless otherwise specified
Income Taxes	'	'
Excess tax benefit related to the exercise of stock options excluded from net operating loss carryforward	$37.30	'
Federal	'	'
Net operating loss carryforwards available to offset future taxable income	'	'
Net operating loss carryforwards	600.9	334.1
State	'	'
Net operating loss carryforwards available to offset future taxable income	'	'
Net operating loss carryforwards	$545.30	$271.40

Income_Taxes_Details_3

Income Taxes (Details 3) (Research and development, USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2013
Research and development	'	'
Tax credit carryforwards available to offset future federal and state income taxes	'	'
Tax credit carryforward	$26.40	$32.10
Limitations on utilization of net operating loss carryforwards and research and development credit carryforwards	'	'
Increase in tax credit carryforward	$9.90	'

Defined_Contribution_Plan_Deta

Defined Contribution Plan (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
401(k) Savings Plan	'	'	'
Employer match of first $6,000 of employee contributions (as a percent)	75.00%	'	'
Amount of employee contributions matched 75% by employer	$6,000	'	'
Continuing operations	'	'	'
401(k) Savings Plan	'	'	'
Compensation cost	$2,800,000	$1,900,000	$600,000
Minimum	'	'	'
401(k) Savings Plan	'	'	'
Employee contribution per calendar year (as a percent of compensation)	1.00%	'	'
Maximum	'	'	'
401(k) Savings Plan	'	'	'
Employee contribution per calendar year (as a percent of compensation)	100.00%	'	'

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)

12 Months Ended

1 Months Ended

1 Months Ended

In Millions, except Share data, unless otherwise specified

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Sep. 30, 2009

Dec. 31, 2012

Dec. 31, 2013

Nov. 30, 2009

Class B common stock

Law firm investor

Law firm investor

Law firm investor

Law firm investor

Law firm investor

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Forest Laboratories, Inc.

Almirall, S.A.

Almirall, S.A.

Almirall, S.A.

Maximum

Maximum

Convertible preferred stock

Maximum

Convertible preferred stock

Related Party Transactions

'

'

'

'

'

'

'

'

'

'

'

'

Legal fees paid

'

$0.10

$0.20

$0.20

'

'

'

'

'

'

'

'

Accounts payable

'

'

'

'

0.1

0.1

'

7.5

'

'

'

'

Issuance of Convertible preferred stock (in shares)

'

'

'

'

'

'

'

'

2,083,333

'

'

681,819

Preferred stock conversion basis

1

'

'

'

'

'

'

'

'

'

'

'

Accounts receivable

'

'

'

'

'

'

$2.70

'

'

$1

$0.10

'

State_Grants_Details

State Grants (Details) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
State Grants	'	'	'
State grant received associated with the Life Science Tax Incentive Program	'	$1.70	$0.90
Minimum period for which jobs must be maintained	'5 years	'	'
Recognized state grant associated with the Life Sciences Tax Incentive Program	$0	'	'

Selected_Quarterly_Financial_D2

Selected Quarterly Financial Data (Unaudited) (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Selected Quarterly Financial Data (Unaudited)	'	'	'	'	'	'	'	'	'	'	'
Collaborative arrangements revenue	$5,031	$4,932	$9,663	$3,255	$26,980	$96,413	$14,604	$12,248	$22,881	$150,245	$65,871
Total cost and expenses	51,769	61,483	69,543	92,088	70,880	48,805	55,438	47,884	274,883	223,007	132,013
Other income (expense), net	-5,248	-5,224	-5,269	-5,069	45	27	31	35	-20,810	138	1,293
Net income (loss)	($51,986)	($61,775)	($65,149)	($93,902)	($43,855)	$47,635	($40,803)	($35,601)	($272,812)	($72,624)	($64,852)
Basic net income (loss) per share (in dollars per share)	($0.43)	($0.51)	($0.57)	($0.87)	($0.41)	$0.44	($0.38)	($0.34)	($2.35)	($0.68)	'
Diluted net income (loss) per share (in dollars per share)	($0.43)	($0.51)	($0.57)	($0.87)	($0.41)	$0.42	($0.38)	($0.34)	($2.35)	($0.68)	'

Subsequent_Events_Details

Subsequent Events (Details) (Subsequent event, Severance, USD $)	0 Months Ended
In Millions, unless otherwise specified	Jan. 08, 2014
Subsequent Events	'
Reduction in workforce (as a percent)	10.00%
Minimum	'
Subsequent Events	'
Estimated restructuring charges	4
Estimated percentage of restructuring charges in cash	85.00%
Maximum	'
Subsequent Events	'
Estimated restructuring charges	4.5
Estimated percentage of restructuring charges in cash	95.00%