Ironwood Pharmaceuticals (IRWD) 10-Q 28 Oct 13 2013 Q3 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	9 Months Ended
	Sep. 30, 2013	Oct. 10, 2013	Oct. 10, 2013
		Class A common stock	Class B common stock
Entity Registrant Name	IRONWOOD PHARMACEUTICALS INC
Entity Central Index Key	1446847
Document Type	10-Q
Document Period End Date	30-Sep-13
Amendment Flag	FALSE
Current Fiscal Year End Date	-19
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		97,477,669	23,425,910
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q3

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Current assets:
Cash and cash equivalents	$144,452	$136,700
Available-for-sale securities	97,938	31,528
Accounts receivable	125	457
Related party accounts receivable, net	2,961	1,030
Inventory	20,561	6,699
Prepaid expenses and other current assets	9,789	8,026
Total current assets	275,826	184,440
Restricted cash	8,147	7,647
Property and equipment, net	37,231	37,537
Other assets	4,639	283
Total assets	325,843	229,907
Current liabilities:
Accounts payable	2,436	14,217
Related party accounts payable, net	5,789	7,509
Accrued research and development costs	3,711	5,664
Accrued expenses	18,800	21,171
Current portion of capital lease obligations	1,115	261
Current portion of deferred rent	2,776	2,735
Current portion of deferred revenue	5,074	3,381
Total current liabilities	39,701	54,938
Capital lease obligations, net of current portion	3,427	308
Deferred rent, net of current portion	9,519	11,593
Deferred revenue, net of current portion	12,684	18,024
Notes payable	174,650
Other liabilities	1,653	992
Commitments and contingencies
Stockholders' equity:
Preferred stock, $0.001 par value, 75,000,000 shares authorized, no shares issued and outstanding
Additional paid-in capital	809,911	648,955
Accumulated deficit	-725,842	-505,016
Accumulated other comprehensive income	19	5
Total stockholders' equity	84,209	144,052
Total liabilities and stockholders' equity	325,843	229,907
Class A common stock
Stockholders' equity:
Common stock	97	78
Class B common stock
Stockholders' equity:
Common stock	$24	$30

Condensed_Consolidated_Balance1

Condensed Consolidated Balance Sheets (Parenthetical) (USD $)	Sep. 30, 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	97,362,406	78,253,074
Common stock, shares outstanding	97,362,406	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	23,539,548	29,512,253
Common stock, shares outstanding	23,539,548	29,512,253

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Condensed Consolidated Statements of Operations
Collaborative arrangements revenue	$4,932	$96,413	$17,850	$123,265
Cost and expenses:
Cost of revenue	2,021		6,670
Research and development	23,016	23,453	79,862	85,201
Selling, general and administrative	30,264	22,846	94,508	59,264
Collaboration expense	6,182	2,506	42,074	7,662
Total cost and expenses	61,483	48,805	223,114	152,127
Income (loss) from operations	-56,551	47,608	-205,264	-28,862
Other income (expense):
Interest expense	-5,265	-14	-15,704	-41
Interest and investment income	41	41	142	134
Other income (expense), net	-5,224	27	-15,562	93
Net income (loss)	($61,775)	$47,635	($220,826)	($28,769)
Basic net income (loss) per share (in dollars per share)	($0.51)	$0.44	($1.93)	($0.27)
Diluted net income (loss) per share (in dollars per share)	($0.51)	$0.42	($1.93)	($0.27)
Weighted average number of common shares used in:
Basic net income (loss) per share (in shares)	120,768,893	107,266,823	114,140,821	106,036,522
Diluted net income (loss) per share (in shares)	120,768,893	114,337,327	114,140,821	106,036,522

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Income (Loss) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Condensed Consolidated Statements of Comprehensive Income (Loss)
Net income (loss)	($61,775)	$47,635	($220,826)	($28,769)
Other comprehensive income:
Unrealized gain on available-for-sale securities	20	16	14	1
Total other comprehensive income	20	16	14	1
Comprehensive income (loss)	($61,755)	$47,651	($220,812)	($28,768)

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Cash Flows (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012
Cash flows from operating activities:
Net loss	($220,826)	($28,769)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	8,647	8,522
Loss on disposal of property and equipment		20
Share-based compensation expense	15,291	12,912
Accretion of discount/premium on investment securities	1,084	840
Non-cash interest expense	1,324
Changes in assets and liabilities:
Accounts receivable and related party accounts receivable	-1,599	470
Restricted cash	-500
Prepaid expenses and other current assets	-3,632	-4,978
Inventory	-10,347	-965
Other assets	120	84
Accounts payable and accrued expenses	-13,867	3,311
Accrued research and development costs	-1,953	-856
Deferred revenue	-3,647	-35,509
Deferred rent	-2,033	-2,256
Other liabilities	661
Net cash used in operating activities	-231,277	-47,174
Cash flows from investing activities:
Purchases of available-for-sale securities	-207,307	-60,896
Sales and maturities of available-for-sale securities	139,827	69,335
Purchases of property and equipment	-5,874	-10,595
Proceeds from sale of property and equipment		9
Net cash used in investing activities	-73,354	-2,147
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 and employee stock purchase plan	7,833	2,881
Payments on capital leases	-499	-203
Net cash provided by financing activities	312,383	87,906
Net increase in cash and cash equivalents	7,752	38,585
Cash and cash equivalents, beginning of period	136,700	87,282
Cash and cash equivalents, end of period	$144,452	$125,867

Nature_of_Business

Nature of Business	9 Months Ended
	Sep. 30, 2013
Nature of Business
Nature of Business	1. Nature of Business
	Overview
	Ironwood Pharmaceuticals, Inc. (the “Company”) is an entrepreneurial pharmaceutical company focused on the discovery, development and commercialization of medicines that improve patients’ lives.
	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 FDA-approved guanylate cyclase type-C (“GC-C”) agonist. The Company and its collaboration partner, Forest Laboratories, Inc. (“Forest”), began commercial sale of 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”), is responsible for marketing 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.
	Astellas Pharma Inc. (“Astellas”), the Company’s partner in Japan, is developing linaclotide for the treatment of patients with IBS-C in its territory. In September 2013, Astellas completed enrollment in a double-blind, placebo controlled, dose-ranging Phase II clinical trial of linaclotide in adult patients with IBS-C.
	In October 2012, the Company entered into a collaboration agreement with AstraZeneca AB (“AstraZeneca”) to co-develop and co-commercialize linaclotide for IBS-C 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 within its indicated population and to expand the product label for additional patient populations and indications, as well as exploring the potential for linaclotide-based combination products. As part of this strategy, the Company and Forest completed a Phase IIIb clinical trial to further characterize the effect of linaclotide on abdominal symptoms in patients with CIC.
	In addition to exploring further linaclotide development opportunities, the Company’s research and development team has generated a pipeline of early development candidates and discovery research in multiple therapeutic areas, including gastrointestinal disease, central nervous system disorders, allergic conditions and cardiovascular disease.
	Basis of Presentation
	The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission on February 21, 2013.
	The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of September 30, 2013, results of its operations for the three and nine months ended September 30, 2013 and 2012 and its cash flows for the nine months ended September 30, 2013 and 2012. The results of operations for the three and nine months ended September 30, 2013 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period. Certain prior-period amounts were reclassified to conform to the current period’s presentation.
	Principles of Consolidation
	The accompanying condensed 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 condensed consolidated financial statements requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets, liabilities, revenues, 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, 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.
	Summary of Significant Accounting Policies
	The Company’s significant accounting policies are described in Note 2, “Summary of Significant Accounting Policies,” in the 2012 Annual Report on Form 10-K.
	New Accounting Pronouncements
	For a discussion of recent accounting pronouncements please refer to Note 2, “Summary of Significant Accounting Policies,” in the 2012 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the three or nine months ended September 30, 2013 that had a material effect on the Company’s condensed consolidated financial statements.

Net_Income_Loss_Per_Share

Net Income (Loss) Per Share	9 Months Ended
	Sep. 30, 2013
Net Income (Loss) Per Share
Net Income (Loss) Per Share	2. 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.
	The following table sets forth the computation of basic and diluted net income (loss) per share (in thousands, except per share amounts):
		Three Months Ended					Nine Months Ended
		September 30,					September 30,
		2013		2012			2013			2012
	Net income (loss)	(61,775	)	$	47,635		$	(220,826	)	$	(28,769	)
	Shares used in calculating basic net income (loss) per common share	120,768,893		107,266,823			114,140,821			106,036,522
	Effect of dilutive securities:
	Options to purchase common stock	—		6,996,544			—			—
	Restricted stock	—		73,960			—			—
	Shares used in calculating diluted net income (loss) per common share	120,768,893		114,337,327			114,140,821			106,036,522
	The following potentially dilutive securities have been excluded from the computation of diluted weighted average shares outstanding as they would be anti-dilutive:
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Options to purchase common stock	20,272,563		9,044,014		20,272,563		18,821,908
	Shares subject to repurchase	22,500		—		22,500		100,458
		20,295,063		9,044,014		20,295,063		18,922,366
	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	9 Months Ended
	Sep. 30, 2013
Collaboration and License Agreements
Collaboration and License Agreements	3. 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 gastrointestinal 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 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 September 30, 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 a $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 11).
	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 Application (“NDA”) for both IBS-C and CIC 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 NDA for both IBS-C and CIC and received milestone payments totaling $85.0 million from Forest in September 2012, accordingly. In accordance with ASU 2010-17, adopted in January 2011, 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.
	The Company recognized no collaborative arrangements revenue from the Forest collaboration agreement during the three and nine months ended September 30, 2013 and $89.5 million and $100.4 million during the three and nine months ended September 30, 2012, respectively.
	As a result of the research and development cost-sharing provisions of the collaboration, the Company recognized approximately $0.6 million and $3.6 million in incremental research and development costs in the three and nine months ended September 30, 2013, respectively, and approximately $0.4 million and $0.8 million in incremental research and development costs in the three and nine months ended September 30, 2012, respectively, 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 the cost to manufacture LINZESS as well as selling, general and administrative and marketing expenses. Net sales are calculated and recorded by Forest and include gross sales net of discounts, rebates, allowances, sales taxes, freight and insurance charges, and other applicable deductions.
	The Company and Forest began commercial sale of LINZESS in December 2012. The following table presents the amounts recorded by the Company for commercial efforts related to LINZESS in the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,				Nine Months Ended September 30,
		2013		2012		2013		2012
	Collaboration expense	$	6,182	$	2,506	$	42,074	$	7,662
	Selling and marketing costs incurred by the Company (1)	8,234		1,204		25,044		3,495
	The Company’s share of net loss	$	14,416	$	3,710	$	67,118	$	11,157
	(1)         Includes only selling and marketing costs attributable to the cost-sharing arrangement with Forest.
	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 gastrointestinal 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 is required to participate on a joint development committee over linaclotide’s development period.
	In May 2009, the Company received a $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 a $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 11).
	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. Remaining 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 and escalate to the mid-forties through April 2017, and thereafter begin in the mid-twenties and escalate to the mid-forties at lower sales thresholds. In each case, these royalty payments are reduced by the transfer price paid for the active pharmaceutical ingredient (“API”) included in the product actually sold in the Almirall territory. 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 $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 $1.9 million payment represented the two $1.0 million milestones, net of foreign tax withholdings.
	The Company recognized approximately $3.0 million and $13.0 million in total collaborative arrangements revenue from the Almirall license agreement during the three and nine months ended September 30, 2013, respectively, including approximately $3.0 million and $11.0 million from the sale of API to Almirall, respectively, $51,000 in each period in royalty revenue and $1.9 million in commercial launch milestones during the nine months ended September 30, 2013. The Company recognized approximately $5.9 million and $20.2 million in total collaborative arrangements revenue from the Almirall license agreement during the three and nine months ended September 30, 2012, respectively, including approximately $13,000 and $2.5 million, respectively, from the sale of API to Almirall.
	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 gastrointestinal 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 did not consider this amendment to be 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 $0.5 million and $1.0 million of revenue in the three and nine months ended September 30, 2013, respectively.
	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, less the transfer price paid for the API included in the product actually sold.
	At September 30, 2013, approximately $17.7 million of the up-front license fee remains deferred.  During the three and nine months ended September 30, 2013, the Company recognized approximately $1.7 million and $4.0 million, respectively, in collaborative arrangements revenue from the Astellas license agreement, including $0.4 million and $0.6 million, respectively, from the sale of API to Astellas.  During the three and nine months ended September 30, 2012, the Company recognized approximately $1.0 million and $2.7 million, respectively, in collaborative arrangements revenue from the Astellas license agreement, including $0.2 million and $0.3 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 September 30, 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 $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 $1.9 million. The Company allocated the Arrangement Consideration of $26.9 million to the non-contingent deliverables based on management’s best estimate of selling price (“BESP”) of each deliverable using the relative selling price method as the Company did not have vendor-specific objective evidence or third-party evidence 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 $26.9 million Arrangement Consideration, $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 $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 $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.
	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. Payments to AstraZeneca are recorded as incremental research and development expense. As a result of the cost-sharing arrangements under the collaboration, the Company recognized approximately $0.7 million and $1.3 million in incremental research and development costs during the three and nine months ended September 30, 2013, respectively.
	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). During the three and nine months ended September 30, 2013, the Company recognized approximately $0.2 million and $0.8 million, respectively, in revenue related to this deliverable.
	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 September 30, 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 three and nine months ended September 30, 2013, the Company incurred $0.7 million and $2.5 million, respectively, in research and development expense associated with the Company’s other collaboration and license agreements. During the three and nine months ended September 30, 2012, the Company incurred $1.0 million and $7.1 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	9 Months Ended
	Sep. 30, 2013
Fair Value of Financial Instruments
Fair Value of Financial Instruments	4. 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 September 30, 2013 and December 31, 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	September 30,		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	$	139,525	$	139,525	$	—	$	—
	Available-for-sale securities:
	U.S. Treasury securities	503		503		—		—
	U.S. government-sponsored securities	97,435		—		97,435		—
	Total	$	237,463	$	140,028	$	97,435	$	—
				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 nine months ended September 30, 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 September 30, 2013 and December 31, 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 September 30, 2013 and December 31, 2012 approximates fair value as it bears interest at a rate approximating a market interest rate.

AvailableforSale_Securities

Available-for-Sale Securities	9 Months Ended
	Sep. 30, 2013
Available-for-Sale Securities
Available-for-Sale Securities	5. Available-for-Sale Securities
	The following tables summarize the available-for-sale securities held at September 30, 2013 and December 31, 2012 (in thousands):
		Amortized Cost		Gross		Gross			Fair Value
				Unrealized		Unrealized
				Gains		Losses
	September 30, 2013:
	U.S. government-sponsored securities	$	97,416	$	19	$	—		$	97,435
	U.S. Treasury securities	503		—		—			503
	Total	$	97,919	$	19	$	—		$	97,938
		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 September 30, 2013 are one year or less.  There were four and three investments in an unrealized loss position at September 30, 2013 and December 31, 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 September 30, 2013 and December 31, 2012 was approximately $4.2 million and $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 an 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 September 30, 2013.
	There were no sales of available-for-sale securities during the nine months ended September 30, 2013 or 2012. 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) have not been 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	9 Months Ended
	Sep. 30, 2013
Inventory
Inventory	6. Inventory
	Inventory consisted of the following at (in thousands):
		September 30,		December 31,
		2013		2012
	Raw materials	$	20,561	$	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., Committee for Medicinal Products for Human Use 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. Inventory at September 30, 2013 and December 31, 2012 represents API that is available for commercial sale.

Property_and_Equipment

Property and Equipment	9 Months Ended
	Sep. 30, 2013
Property and Equipment
Property and Equipment	7. Property and Equipment
	Property and equipment, net consisted of the following (in thousands):
		September 30,			December 31,
		2013			2012
	Laboratory equipment	$	17,282		$	16,315
	Computer and office equipment	6,766			6,476
	Furniture and fixtures	2,449			2,449
	Software	13,601			11,047
	Construction in process	1,286			1,460
	Leased vehicles	4,472			—
	Leasehold improvements	36,805			36,770
		82,661			74,517
	Less accumulated depreciation and amortization	(45,430		)	(36,980			)
		$	37,231		$		$37,537
	In the second and third quarter of 2013, the Company entered into capital leases for the vehicle fleet for its field-based sales force and medical science liaisons. As a result of these lease agreements, the Company’s commitments for the years ending December 31, 2013 (3 months), 2014, 2015 and 2016 increased by $0.3 million, $1.2 million, $1.2 million and $2.1 million, respectively.

Accrued_Expenses

Accrued Expenses	9 Months Ended
	Sep. 30, 2013
Accrued Expenses
Accrued Expenses	8. Accrued Expenses
	Accrued expenses consisted of the following (in thousands):
		September 30,		December 31,
		2013		2012
	Salaries and benefits	$	13,114	$	14,594
	Professional fees	1,393		1,031
	Accrued interest	855		—
	Other	3,438		5,546
		$	18,800	$	21,171

Notes_Payable

Notes Payable	9 Months Ended
	Sep. 30, 2013
Notes Payable
Notes Payable	9. 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 the June 15, 2024, the final legal maturity date. The Company does not expect to make significant principal payments within twelve months following September 30, 2013 and, as such, the outstanding principal balance was classified as a long term liability as of September 30, 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 occurs prior to January 1, 2014, the Company will pay 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 $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 $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 discount 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 $185.5 million as of September 30, 2013, and was determined using Level 3 inputs, including a quoted rate.

Employee_Stock_Benefit_Plans

Employee Stock Benefit Plans	9 Months Ended
	Sep. 30, 2013
Employee Stock Benefit Plans
Employee Stock Benefit Plans	10. Employee Stock Benefit Plans
	The Company has several share-based compensation plans under which stock options, restricted stock, restricted stock units, and other share-based awards are available for grant to employees, directors and consultants of the Company.
	The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013		2012
	Research and development	$	2,349		$	2,648		$	7,274	$	6,676
	Selling, general and administrative	2,850			2,487			8,017		6,236
		$	5,199		$	5,135		$	15,291	$	12,912
	A summary of stock option activity for the nine months ended September 30, 2013 is as follows:
		Number of Shares		Weighted-Average
				Exercise Price
	Outstanding at December 31, 2012	19,539,429		$	7.75
	Granted	2,932,870		13.09
	Exercised	(1,700,135	)	3.47
	Cancelled	(499,601	)	12.29
	Outstanding at September 30, 2013	20,272,563		8.77
	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 three and nine months ended September 30, 2013 and 2012:
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Expected volatility	46.8	%	47.1	%	46.4	%	49.9	%
	Expected term (in years)	6.5		6.5		6.5		6.5
	Risk-free interest rate	2.1	%	1	%	1.4	%	1.3	%
	Expected dividend yield	—	%	—	%	—	%	—	%

Related_Party_Transactions

Related Party Transactions	9 Months Ended
	Sep. 30, 2013
Related Party Transactions
Related Party Transactions	11. Related Party Transactions
	The Company has and currently obtains legal services from a law firm that is an investor in the Company. The Company paid approximately $19,000 and $74,000 in legal fees to this investor during the three and nine months ended September 30, 2013, respectively, and approximately $23,000 and $182,000 during the three and nine months ended September 30, 2012, respectively. At September 30, 2013 and December 31, 2012, the Company had approximately $78,000 and $23,000 of accounts payable due to this related party, respectively.
	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 3). 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 initial public offering 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 September 30, 2013, the Company had approximately $3.0 million in related party accounts receivable associated with Almirall and $5.7 million in related party accounts payable, net of related party accounts receivable, 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.

Public_Offerings

Public Offerings	9 Months Ended
	Sep. 30, 2013
Public Offerings
Public Offerings	12. Public Offerings
	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.
	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 this offering, the Company received aggregate net proceeds, after underwriting discounts and commissions and other offering expenses, of approximately $85.2 million.

Nature_of_Business_Policies

Nature of Business (Policies)	9 Months Ended
	Sep. 30, 2013
Nature of Business
Basis of Presentation	Basis of Presentation
	The accompanying condensed consolidated financial statements and the related disclosures are unaudited and have been prepared in accordance with accounting principles generally accepted in the U.S. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission on February 21, 2013.
	The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position as of September 30, 2013, results of its operations for the three and nine months ended September 30, 2013 and 2012 and its cash flows for the nine months ended September 30, 2013 and 2012. The results of operations for the three and nine months ended September 30, 2013 are not necessarily indicative of the results that may be expected for the full year or any other subsequent interim period. Certain prior-period amounts were reclassified to conform to the current period’s presentation.
Principles of Consolidation	Principles of Consolidation
	The accompanying condensed 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 condensed consolidated financial statements requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets, liabilities, revenues, 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, 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.
New Accounting Pronouncements	New Accounting Pronouncements
	For a discussion of recent accounting pronouncements please refer to Note 2, “Summary of Significant Accounting Policies,” in the 2012 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the three or nine months ended September 30, 2013 that had a material effect on the Company’s condensed consolidated financial statements.

Net_Income_Loss_Per_Share_Tabl

Net Income (Loss) Per Share (Tables)	9 Months Ended
	Sep. 30, 2013
Net Income (Loss) Per Share
Schedule of computation of basic and diluted net income (loss) per share	The following table sets forth the computation of basic and diluted net income (loss) per share (in thousands, except per share amounts):
		Three Months Ended					Nine Months Ended
		September 30,					September 30,
		2013		2012			2013			2012
	Net income (loss)	(61,775	)	$	47,635		$	(220,826	)	$	(28,769	)
	Shares used in calculating basic net income (loss) per common share	120,768,893		107,266,823			114,140,821			106,036,522
	Effect of dilutive securities:
	Options to purchase common stock	—		6,996,544			—			—
	Restricted stock	—		73,960			—			—
	Shares used in calculating diluted net income (loss) per common share	120,768,893		114,337,327			114,140,821			106,036,522
Schedule of potentially dilutive securities that have been excluded from computation of diluted weighted average shares outstanding
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Options to purchase common stock	20,272,563		9,044,014		20,272,563		18,821,908
	Shares subject to repurchase	22,500		—		22,500		100,458
		20,295,063		9,044,014		20,295,063		18,922,366

Collaboration_and_License_Agre1

Collaboration and License Agreements (Tables)	9 Months Ended
	Sep. 30, 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 three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,				Nine Months Ended September 30,
		2013		2012		2013		2012
	Collaboration expense	$	6,182	$	2,506	$	42,074	$	7,662
	Selling and marketing costs incurred by the Company (1)	8,234		1,204		25,044		3,495
	The Company’s share of net loss	$	14,416	$	3,710	$	67,118	$	11,157
	(1)         Includes only selling and marketing costs attributable to the cost-sharing arrangement with Forest.

Fair_Value_of_Financial_Instru1

Fair Value of Financial Instruments (Tables)	9 Months Ended
	Sep. 30, 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	September 30,		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	$	139,525	$	139,525	$	—	$	—
	Available-for-sale securities:
	U.S. Treasury securities	503		503		—		—
	U.S. government-sponsored securities	97,435		—		97,435		—
	Total	$	237,463	$	140,028	$	97,435	$	—
				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)	9 Months Ended
	Sep. 30, 2013
Available-for-Sale Securities
Schedule of summary of available-for-sale securities	The following tables summarize the available-for-sale securities held at September 30, 2013 and December 31, 2012 (in thousands):
		Amortized Cost		Gross		Gross			Fair Value
				Unrealized		Unrealized
				Gains		Losses
	September 30, 2013:
	U.S. government-sponsored securities	$	97,416	$	19	$	—		$	97,435
	U.S. Treasury securities	503		—		—			503
	Total	$	97,919	$	19	$	—		$	97,938
		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)	9 Months Ended
	Sep. 30, 2013
Inventory
Schedule of Inventory	Inventory consisted of the following at (in thousands):
		September 30,		December 31,
		2013		2012
	Raw materials	$	20,561	$	6,699

Property_and_Equipment_Tables

Property and Equipment (Tables)	9 Months Ended
	Sep. 30, 2013
Property and Equipment
Schedule of property and equipment	Property and equipment, net consisted of the following (in thousands):
		September 30,			December 31,
		2013			2012
	Laboratory equipment	$	17,282		$	16,315
	Computer and office equipment	6,766			6,476
	Furniture and fixtures	2,449			2,449
	Software	13,601			11,047
	Construction in process	1,286			1,460
	Leased vehicles	4,472			—
	Leasehold improvements	36,805			36,770
		82,661			74,517
	Less accumulated depreciation and amortization	(45,430		)	(36,980			)
		$	37,231		$		$37,537

Accrued_Expenses_Tables

Accrued Expenses (Tables)	9 Months Ended
	Sep. 30, 2013
Accrued Expenses
Schedule of accrued expenses	Accrued expenses consisted of the following (in thousands):
		September 30,		December 31,
		2013		2012
	Salaries and benefits	$	13,114	$	14,594
	Professional fees	1,393		1,031
	Accrued interest	855		—
	Other	3,438		5,546
		$	18,800	$	21,171

Notes_Payable_Tables

Notes Payable (Tables)	9 Months Ended
	Sep. 30, 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	%

Employee_Stock_Benefit_Plans_T

Employee Stock Benefit Plans (Tables)	9 Months Ended
	Sep. 30, 2013
Employee Stock Benefit Plans
Share-based compensation expense reflected in the condensed consolidated statements of operations	The following table summarizes share-based compensation expense reflected in the condensed consolidated statements of operations for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013		2012
	Research and development	$	2,349		$	2,648		$	7,274	$	6,676
	Selling, general and administrative	2,850			2,487			8,017		6,236
		$	5,199		$	5,135		$	15,291	$	12,912
Summary of stock option activity
		Number of Shares		Weighted-Average
				Exercise Price
	Outstanding at December 31, 2012	19,539,429		$	7.75
	Granted	2,932,870		13.09
	Exercised	(1,700,135	)	3.47
	Cancelled	(499,601	)	12.29
	Outstanding at September 30, 2013	20,272,563		8.77
Schedule of weighted-average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Expected volatility	46.8	%	47.1	%	46.4	%	49.9	%
	Expected term (in years)	6.5		6.5		6.5		6.5
	Risk-free interest rate	2.1	%	1	%	1.4	%	1.3	%
	Expected dividend yield	—	%	—	%	—	%	—	%

Net_Income_Loss_Per_Share_Deta

Net Income (Loss) Per Share (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Computation of basic and diluted net income (loss) per share
Net income (loss)	($61,775)	$47,635	($220,826)	($28,769)
Shares used in calculating basic net income (loss) per common share	120,768,893	107,266,823	114,140,821	106,036,522
Effect of dilutive securities:
Shares used in calculating diluted net income (loss) per common share	120,768,893	114,337,327	114,140,821	106,036,522
Options to purchase common stock
Effect of dilutive securities:
Dilutive securities (in shares)		6,996,544
Restricted stock
Effect of dilutive securities:
Dilutive securities (in shares)		73,960

Net_Income_Loss_Per_Share_Deta1

Net Income (Loss) Per Share (Details 2)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Potentially dilutive securities
Dilutive securities excluded from the computation of diluted weighted average shares outstanding	20,295,063	9,044,014	20,295,063	18,922,366
Options to purchase common stock
Potentially dilutive securities
Dilutive securities excluded from the computation of diluted weighted average shares outstanding	20,272,563	9,044,014	20,272,563	18,821,908
Shares subject to repurchase
Potentially dilutive securities
Dilutive securities excluded from the computation of diluted weighted average shares outstanding	22,500		22,500	100,458

Collaboration_and_License_Agre2

Collaboration and License Agreements (Details) (USD $)

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

9 Months Ended

1 Months Ended

9 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2007

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2009

Sep. 30, 2013

Sep. 30, 2012

Aug. 31, 2012

Oct. 31, 2011

Jul. 31, 2009

Sep. 30, 2008

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 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.

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

6,182,000

2,506,000

42,074,000

7,662,000

6,182,000

2,506,000

42,074,000

7,662,000

Selling and marketing costs incurred by the Company

8,234,000

1,204,000

25,044,000

3,495,000

The Company's share of net loss

14,416,000

3,710,000

67,118,000

11,157,000

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

4,932,000

96,413,000

17,850,000

123,265,000

0

89,500,000

0

100,400,000

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

$600,000

$400,000

$3,600,000

$800,000

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

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

1 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

31-May-09

Apr. 30, 2009

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Nov. 30, 2009

Apr. 30, 2009

Nov. 30, 2010

Jun. 30, 2013

Apr. 30, 2009

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

Development milestones

item

Convertible preferred stock

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

3,000,000

13,000

11,000,000

2,500,000

Revenue recognized in royalty payments

51,000

51,000

Revenue recognized in commercial launch milestones

1,900,000

Collaborative arrangements revenue

4,932,000

96,413,000

17,850,000

123,265,000

3,000,000

5,900,000

13,000,000

20,200,000

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

$4,000,000

Collaboration_and_License_Agre4

Collaboration and License Agreements (Details 3) (USD $)	1 Months Ended		3 Months Ended		9 Months Ended
	Mar. 31, 2013	Nov. 30, 2009	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Collaboration and License Agreements
Collaborative arrangements revenue			$4,932,000	$96,413,000	$17,850,000	$123,265,000
Astellas Pharma Inc.
Collaboration and License Agreements
Up-front fee received		30,000,000
Estimated development period prior to assessment	115 months
Estimated development period	85 months
Revenue recognized as a result of revised estimate of development period			500,000		1,000,000
Up-front license fee deferred			17,700,000		17,700,000
Collaborative arrangements revenue			1,700,000	1,000,000	4,000,000	2,700,000
Revenue recognized from sale of API			400,000	200,000	600,000	300,000
Astellas Pharma Inc. | Additional development milestones | Maximum
Collaboration and License Agreements
Total milestone payments to be received					45,000,000
Astellas Pharma Inc. | Phase 3 milestones
Collaboration and License Agreements
Milestone payment to be received by company upon milestone achievement					15,000,000
Astellas Pharma Inc. | Japanese NDA equivalent filing milestone
Collaboration and License Agreements
Milestone payment to be received by company upon milestone achievement					15,000,000
Astellas Pharma Inc. | Approval of Japanese NDA equivalent filing milestone
Collaboration and License Agreements
Milestone payment to be received by company upon milestone achievement					$15,000,000

Collaboration_and_License_Agre5

Collaboration and License Agreements (Details 4) (USD $)	3 Months Ended		9 Months Ended		1 Months Ended	3 Months Ended	9 Months Ended	1 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Oct. 31, 2012	Sep. 30, 2013	Sep. 30, 2013	Oct. 31, 2012	Oct. 31, 2012
					AstraZeneca	AstraZeneca	AstraZeneca	AstraZeneca	AstraZeneca
								Sales milestones	Commercialization milestone
Collaboration and License Agreements
Prior notice period to terminate the agreement					180 days
Up-front fee received					$25,000,000
Milestone payment to be received by company upon milestone achievement								125,000,000
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%
Collaborative arrangements revenue	4,932,000	96,413,000	17,850,000	123,265,000		200,000	800,000
Net cost sharing offset or incremental expense related to research and development expense						$700,000	$1,300,000
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 $)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Collaboration and License Agreements
Research and development expense	$23,016,000	$23,453,000	$79,862,000	$85,201,000
Other Collaboration and License Agreements
Collaboration and License Agreements
Research and development expense	700,000	1,000,000	2,500,000	7,100,000
Aggregate up-front fee paid			5,800,000
Contingent milestone payable per product, maximum			114,500,000
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 $)	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2012
In Thousands, unless otherwise specified
Description
Available-for-sale securities	$97,938	$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	237,463	145,396
Recurring basis | Fair Value | Money market funds
Description
Cash and cash equivalents	139,525	111,368
Recurring basis | Fair Value | U.S. Treasury securities
Description
Available-for-sale securities	503	15,052
Recurring basis | Fair Value | U.S. government-sponsored securities
Description
Cash and cash equivalents		2,500
Available-for-sale securities	97,435	16,476
Recurring basis | Quoted Prices in Active Markets for Identical Assets (Level 1)
Description
Total assets fair value	140,028	126,420
Recurring basis | Quoted Prices in Active Markets for Identical Assets (Level 1) | Money market funds
Description
Cash and cash equivalents	139,525	111,368
Recurring basis | Quoted Prices in Active Markets for Identical Assets (Level 1) | U.S. Treasury securities
Description
Available-for-sale securities	503	15,052
Recurring basis | Significant Other Observable Inputs (Level 2)
Description
Total assets fair value	97,435	18,976
Recurring basis | Significant Other Observable Inputs (Level 2) | U.S. government-sponsored securities
Description
Cash and cash equivalents		2,500
Available-for-sale securities	$97,435	$16,476

AvailableforSale_Securities_De

Available-for-Sale Securities (Details) (USD $)	9 Months Ended		12 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Dec. 31, 2012
	item		item
Available-for-Sale Securities
Amortized Cost	$97,919,000		$31,523,000
Gross Unrealized Gains	19,000		6,000
Gross Unrealized Losses			-1,000
Fair Value	97,938,000		31,528,000
Contractual maturity period, maximum	1 year
Number of investments classified as available-for-sale securities in an unrealized loss position	4		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	4,200,000		3,000,000
Proceeds from sales of available-for-sale securities	0	0
U.S. government-sponsored securities
Available-for-Sale Securities
Amortized Cost	97,416,000		16,472,000
Gross Unrealized Gains	19,000		5,000
Gross Unrealized Losses			-1,000
Fair Value	97,435,000		16,476,000
U.S. Treasury securities
Available-for-Sale Securities
Amortized Cost	503,000		15,051,000
Gross Unrealized Gains			1,000
Fair Value	$503,000		$15,052,000

Inventory_Details

Inventory (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Inventory
Raw materials	$20,561	$6,699

Property_and_Equipment_Details

Property and Equipment (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
Property and equipment
Property and equipment, gross	$82,661,000	$74,517,000
Less accumulated depreciation and amortization	-45,430,000	-36,980,000
Property and equipment, net	37,231,000	37,537,000
Increase in capital lease commitments
2013 (3 months)	300,000
2014	1,200,000
2015	1,200,000
2016	2,100,000
Laboratory equipment
Property and equipment
Property and equipment, gross	17,282,000	16,315,000
Computer and office equipment
Property and equipment
Property and equipment, gross	6,766,000	6,476,000
Furniture and fixtures
Property and equipment
Property and equipment, gross	2,449,000	2,449,000
Software
Property and equipment
Property and equipment, gross	13,601,000	11,047,000
Construction in process
Property and equipment
Property and equipment, gross	1,286,000	1,460,000
Leased vehicles
Property and equipment
Property and equipment, gross	4,472,000
Leasehold improvements
Property and equipment
Property and equipment, gross	$36,805,000	$36,770,000

Accrued_Expenses_Details

Accrued Expenses (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Accrued Expenses
Salaries and benefits	$13,114	$14,594
Professional fees	1,393	1,031
Accrued interest	855
Other	3,438	5,546
Total accrued expense	$18,800	$21,171

Notes_Payable_Details

Notes Payable (Details) (USD $)	0 Months Ended	9 Months Ended
	Jan. 04, 2013	Sep. 30, 2013
Notes Payable
Upfront cash proceeds		$175,000,000
Notes Payable
Notes Payable
Aggregate principal amount of notes issued in private placement	175,000,000
Annual interest rate of notes (as a percent)	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%
Upfront cash proceeds	175,000,000
Discount on issuance of debt	400,000
Debt issuance costs capitalized	7,300,000
Estimated fair value		$185,500,000
Notes Payable | From and including January 1, 2014 to and including December 31, 2014
Notes Payable
Payment start date		1-Jan-14
Payment end date		31-Dec-14
Redemption Percentage		112.00%
Notes Payable | From and including January 1, 2015 to and including December 31, 2015
Notes Payable
Payment start date		1-Jan-15
Payment end date		31-Dec-15
Redemption Percentage		105.50%
Notes Payable | From and including January 1, 2016 to and including December 31, 2016
Notes Payable
Payment start date		1-Jan-16
Payment end date		31-Dec-16
Redemption Percentage		102.75%
Notes Payable | From and including January 1, 2017 and thereafter
Notes Payable
Payment start date		1-Jan-17
Redemption Percentage		100.00%

Employee_Stock_Benefit_Plans_D

Employee Stock Benefit Plans (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Share-based compensation is reflected in the condensed consolidated statements of operations
Share-based compensation	$5,199	$5,135	$15,291	$12,912
Research and development
Share-based compensation is reflected in the condensed consolidated statements of operations
Share-based compensation	2,349	2,648	7,274	6,676
Selling, general and administrative
Share-based compensation is reflected in the condensed consolidated statements of operations
Share-based compensation	$2,850	$2,487	$8,017	$6,236

Employee_Stock_Benefit_Plans_D1

Employee Stock Benefit Plans (Details 2) (Stock options, USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Stock options
Number of Shares
Outstanding at the beginning of the period (in shares)			19,539,429
Granted (in shares)			2,932,870
Exercised (in shares)			-1,700,135
Cancelled (in shares)			-499,601
Outstanding at the end of the period (in shares)	20,272,563		20,272,563
Weighted-Average Exercise Price
Outstanding at the beginning of the period (in dollars per share)			$7.75
Granted (in dollars per share)			$13.09
Exercised (in dollars per share)			$3.47
Cancelled (in dollars per share)			$12.29
Outstanding at the end of the period (in dollars per share)	$8.77		$8.77
Weighted-average assumptions used to estimate the fair value of the stock options using the Black-Scholes option-pricing model
Expected volatility (as a percent)	46.80%	47.10%	46.40%	49.90%
Expected term	6 years 6 months	6 years 6 months	6 years 6 months	6 years 6 months
Risk-free interest rate (as a percent)	2.10%	1.00%	1.40%	1.30%

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)

9 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

1 Months Ended

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2009

Sep. 30, 2013

Dec. 31, 2012

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.

Convertible preferred stock

Convertible preferred stock

Related Party Transactions

Legal fees paid

$19,000

$23,000

$74,000

$182,000

Accounts payable

78,000

78,000

23,000

5,700,000

7,500,000

Issuance of Convertible preferred stock (in shares)

2,083,333

681,819

Preferred stock conversion basis

1

Accounts receivable

$3,000,000

$1,000,000

Public_Offerings_Details

Public Offerings (Details) (USD $)	9 Months Ended		1 Months Ended	3 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Feb. 29, 2012	Jun. 30, 2013
			Class A common stock	Class A common stock
Public offerings
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