Vertex Pharmaceuticals (VRTX) 10-Q 4 Aug 15 2015 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2015	Jul. 24, 2015
Document and Entity Information [Abstract]
Entity Registrant Name	VERTEX PHARMACEUTICALS INC / MA
Entity Central Index Key	875,320
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2015
Document Fiscal Year Focus	2,015
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding		244,655,527

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Revenues:
Product revenues, net	$ 160,388	$ 122,319	$ 291,263	$ 225,780
Royalty revenues	5,077	13,015	11,869	23,748
Collaborative revenues	611	3,087	1,453	7,344
Total revenues	166,076	138,421	304,585	256,872
Costs and expenses:
Cost of product revenues	15,409	9,655	24,790	18,227
Royalty expenses	1,451	7,645	4,377	14,549
Research and development expenses	223,858	224,487	439,457	463,104
Sales, general and administrative expenses	94,394	77,446	180,254	151,658
Restructuring expenses (income)	2,128	(270)	(1,144)	5,918
Total costs and expenses	337,240	318,963	647,734	653,456
Loss from operations	(171,164)	(180,542)	(343,149)	(396,584)
Interest expense, net	(21,111)	(15,585)	(42,418)	(31,302)
Other income (expenses), net	1,414	37,731	(3,699)	38,182
Loss from continuing operations before provision for income taxes	(190,861)	(158,396)	(389,266)	(389,704)
Provision for income taxes	30,131	693	30,430	1,496
Loss from continuing operations	(220,992)	(159,089)	(419,696)	(391,200)
Loss from discontinued operations, net of tax benefit of $0	0	(293)	0	(639)
Net loss	(220,992)	(159,382)	(419,696)	(391,839)
Loss attributable to noncontrolling interest	32,144	0	32,242	0
Net loss attributable to Vertex	(188,848)	(159,382)	(387,454)	(391,839)
Loss from continuing operations	(188,848)	(159,089)	(387,454)	(391,200)
Loss from discontinued operations	$ 0	$ (293)	$ 0	$ (639)
Net loss from continuing operations:
Net loss per share from continuing operations, basic (usd per share)	$ (0.78)	$ (0.68)	$ (1.61)	$ (1.68)
Net loss per share from continuing operations, diluted (usd per share)	(0.78)	(0.68)	(1.61)	(1.68)
Net loss from discontinued operations:
Net loss from discontinued operations, basic (usd per share)	0	0	0	0
Net loss from discontinued operations, diluted (usd per share)	0	0	0	0
Net loss:
Basic (usd per share)	(0.78)	(0.68)	(1.61)	(1.68)
Diluted (usd per share)	$ (0.78)	$ (0.68)	$ (1.61)	$ (1.68)
Shares used in per share calculations:
Basic (in shares)	240,757	233,808	240,129	233,353
Diluted (in shares)	240,757	233,808	240,129	233,353

Condensed Consolidated Stateme3

Condensed Consolidated Statements of Operations (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Income Statement [Abstract]
Tax effect of discontinued operations	$ 0	$ 0	$ 0	$ 0

Condensed Consolidated Stateme4

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Net loss	$ (220,992)	$ (159,382)	$ (419,696)	$ (391,839)
Changes in other comprehensive loss:
Unrealized holding (losses) gains on marketable securities	(46)	82	130	55
Unrealized losses on foreign currency forward contracts	(4,280)	(89)	(3,974)	(125)
Foreign currency translation adjustment	1,828	281	1,220	353
Total changes in other comprehensive loss	(2,498)	274	(2,624)	283
Comprehensive loss	(223,490)	(159,108)	(422,320)	(391,556)
Comprehensive loss attributable to noncontrolling interest	32,144	0	32,242	0
Comprehensive loss attributable to Vertex	$ (191,346)	$ (159,108)	$ (390,078)	$ (391,556)

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Current assets:
Cash and cash equivalents	$ 870,543	$ 625,259
Marketable securities, available for sale	145,907	761,847
Restricted cash and cash equivalents (VIE)	88,318	8,418
Accounts receivable, net	94,519	75,964
Inventories	42,113	30,848
Prepaid expenses and other current assets	53,289	44,175
Total current assets	1,294,689	1,546,511
Property and equipment, net	713,378	715,812
Intangible assets	284,340	29,000
Goodwill	50,384	39,915
Restricted cash	22,146	176
Other assets	9,136	3,265
Total assets	2,374,073	2,334,679
Current liabilities:
Accounts payable	72,703	71,194
Accrued expenses	206,030	209,676
Deferred revenues, current portion	14,930	17,468
Accrued restructuring expenses, current portion	10,166	33,107
Capital lease obligations, current portion	13,921	17,806
Senior secured term loan, current portion	42,873	14,206
Other liabilities, current portion	13,200	4,797
Total current liabilities	373,823	368,254
Deferred revenues, excluding current portion	21,019	27,808
Accrued restructuring expenses, excluding current portion	9,677	12,748
Capital lease obligations, excluding current portion	42,900	39,293
Deferred tax liability	112,413	15,044
Fan Pier lease obligation, excluding current portion	472,834	473,073
Senior secured term loan, excluding current portion	251,939	280,569
Other liabilities, excluding current portion	41,252	21,707
Total liabilities	$ 1,325,857	$ 1,238,496
Commitments and contingencies
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at June 30, 2015 and December 31, 2014	$ 0	$ 0
Common stock, $0.01 par value; 500,000,000 and 300,000,000 shares authorized at June 30, 2015 and December 31, 2014, respectively; 244,341,701 and 241,764,398 shares issued and outstanding at June 30, 2015 and December 31, 2014, respectively	2,406	2,385
Additional paid-in capital	5,987,169	5,777,154
Accumulated other comprehensive (loss) income	(1,707)	917
Accumulated deficit	(5,092,904)	(4,705,450)
Total Vertex shareholders' equity	894,964	1,075,006
Noncontrolling interest	153,252	21,177
Total shareholders’ equity	1,048,216	1,096,183
Total liabilities and shareholders’ equity	$ 2,374,073	$ 2,334,679

Condensed Consolidated Balance6

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2015	Dec. 31, 2014
Statement of Financial Position [Abstract]
Preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	1,000,000	1,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized	500,000,000	300,000,000
Common stock, shares issued	244,341,701	241,764,398
Common stock, shares outstanding	244,341,701	241,764,398

Condensed Consolidated Stateme7

Condensed Consolidated Statements of Shareholders' Equity and Noncontrolling Interest - USD ($) shares in Thousands, $ in Thousands	Total	Total Vertex Shareholders' Equity	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Noncontrolling Interest
Balance (shares) at Dec. 31, 2013			233,789
Balance at Dec. 31, 2013	$ 1,356,405	$ 1,356,405	$ 2,320	$ 5,321,286	$ (306)	$ (3,966,895)	$ 0
Increase (Decrease) in Stockholders' Equity
Other comprehensive income (loss), net of tax	283	283			283
Net loss	(391,839)	(391,839)				(391,839)	0
Issuance of common stock under benefit plans (shares)			3,542
Issuance of common stock under benefit plans	117,947	117,947	$ 27	117,920
Stock-based compensation	89,473	89,473		89,473
Balance (shares) at Jun. 30, 2014			237,331
Balance at Jun. 30, 2014	1,172,269	1,172,269	$ 2,347	5,528,679	(23)	(4,358,734)	0
Balance (shares) at Dec. 31, 2014			241,764
Balance at Dec. 31, 2014	1,096,183	1,075,006	$ 2,385	5,777,154	917	(4,705,450)	21,177
Increase (Decrease) in Stockholders' Equity
Other comprehensive income (loss), net of tax	(2,624)	(2,624)			(2,624)
Net loss	(419,696)	(387,454)				(387,454)	(32,242)
Issuance of common stock under benefit plans (shares)			2,578
Issuance of common stock under benefit plans	87,354	87,354	$ 21	87,333
Stock-based compensation	122,682	122,682		122,682
Noncontrolling interest upon consolidation	164,317	0					164,317
Balance (shares) at Jun. 30, 2015			244,342
Balance at Jun. 30, 2015	$ 1,048,216	$ 894,964	$ 2,406	$ 5,987,169	$ (1,707)	$ (5,092,904)	$ 153,252

Condensed Consolidated Stateme8

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014
Cash flows from operating activities:
Net loss	$ (419,696)	$ (391,839)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization expense	30,428	29,960
Stock-based compensation expense	120,645	89,024
Deferred income taxes	6,346	0
Other non-cash items, net	6,045	22
Changes in operating assets and liabilities:
Accounts receivable, net	(21,197)	2,518
Inventories	(9,426)	1,194
Prepaid expenses and other assets	(15,397)	(17,538)
Accounts payable	(3,033)	7,671
Accrued expenses and other liabilities	38,206	(9,459)
Accrued restructuring expense	(26,012)	(9,369)
Deferred revenues	(9,303)	(5,866)
Net cash used in operating activities	(302,394)	(303,682)
Cash flows from investing activities:
Purchases of marketable securities	(125,655)	(703,977)
Sales and maturities of marketable securities	741,725	801,206
Payment for acquisition of variable interest entity	(80,000)	0
Expenditures for property and equipment	(23,978)	(27,227)
(Increase) decrease in restricted cash and cash equivalents	(21,975)	1
Decrease in restricted cash and cash equivalents (VIE)	2,277	0
Decrease (increase) in other assets	87	(528)
Net cash provided by investing activities	492,481	69,475
Cash flows from financing activities:
Issuances of common stock from employee benefit plans	87,850	117,947
Payments on capital lease obligations	(14,441)	(11,884)
Proceeds from capital lease financing	13,386	0
Payments on Fan Pier lease obligation	(30,292)	(30,292)
Payments returned related to Fan Pier lease obligation	0	8,050
Net cash provided by (used in) financing activities	56,503	83,821
Effect of changes in exchange rates on cash	(1,306)	1,645
Net increase (decrease) in cash and cash equivalents	245,284	(148,741)
Cash and cash equivalents—beginning of period	625,259	569,299
Cash and cash equivalents—end of period	870,543	420,558
Supplemental disclosure of cash flow information:
Cash paid for interest	12,777	31,933
Cash paid for income taxes	1,022	798
Capitalization of costs related to Fan Pier lease obligation	0	25,564
Assets acquired under capital lease	0	8,985
Issuances of common stock exercises from employee benefit plans receivable	$ 166	$ 0

Basis of Presentation and Accou

Basis of Presentation and Accounting Policies	6 Months Ended
	Jun. 30, 2015
Accounting Policies [Abstract]
Basis of Presentation and Accounting Policies	Basis of Presentation and Accounting Policies Basis of Presentation The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated ("Vertex" or the "Company") in accordance with accounting principles generally accepted in the United States of America ("GAAP"). The condensed consolidated financial statements reflect the operations of (i) the Company, (ii) its wholly-owned subsidiaries and (iii) consolidated variable interest entities (VIEs). All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended June 30, 2015 and 2014 . The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, 2014 , which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2014 that was filed with the Securities and Exchange Commission (the “SEC”) on February 13, 2015 (the "2014 Annual Report on Form 10-K"). Use of Estimates and Summary of Significant Accounting Policies The preparation of condensed consolidated financial statements in accordance with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with the calculation of revenues, inventories, research and development expenses, stock-based compensation expense, restructuring expense, the fair value of intangible assets, goodwill, noncontrolling interest, the consolidation of VIEs, leases and the provision for or benefit from income taxes. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. The Company's significant accounting policies are described in Note A, "Nature of Business and Accounting Policies," in the 2014 Annual Report on Form 10-K. Recent Accounting Pronouncements For a discussion of recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2014 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the six months ended June 30, 2015 that had a material effect on its condensed consolidated financial statements.

Product Revenues, Net

Product Revenues, Net	6 Months Ended
	Jun. 30, 2015
Product Revenues [Abstract]
Product Revenues, Net	Product Revenues, Net The Company sells its products principally to a limited number of specialty pharmacy providers and selected regional wholesalers in North America as well as government-owned and supported customers in international markets (collectively, its “Customers”). The Company's Customers in North America subsequently resell the products to patients and health care providers. The Company recognizes net revenues from product sales upon delivery to the Customer as long as (i) there is persuasive evidence that an arrangement exists between the Company and the Customer, (ii) collectibility is reasonably assured and (iii) the price is fixed or determinable. In order to conclude that the price is fixed or determinable, the Company must be able to (i) calculate its gross product revenues from sales to Customers and (ii) reasonably estimate its net product revenues upon delivery to its Customer's locations. The Company calculates gross product revenues based on the price that the Company charges its Customers. The Company estimates its net product revenues by deducting from its gross product revenues (a) trade allowances, such as invoice discounts for prompt payment and Customer fees, (b) estimated government and private payor rebates, chargebacks and discounts, (c) estimated reserves for expected product returns and (d) estimated costs of incentives offered to certain indirect customers, including patients. The Company makes significant estimates and judgments that materially affect the Company's recognition of net product revenues. In certain instances, the Company may be unable to reasonably conclude that the price is fixed or determinable at the time of delivery, in which case it defers the recognition of revenues. Once the Company is able to determine that the price is fixed or determinable, it recognizes the revenues associated with the units in which revenue recognition was deferred. The following table summarizes activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2015 : Trade Rebates, Product Other Total (in thousands) Balance at December 31, 2014 $ 1,463 $ 29,102 $ 4,713 $ 745 $ 36,023 Provision related to current period sales 2,865 20,305 181 1,251 24,602 Adjustments related to prior period sales (86 ) (5,958 ) (975 ) (235 ) (7,254 ) Credits/payments made (2,985 ) (13,654 ) (3,194 ) (1,105 ) (20,938 ) Balance at June 30, 2015 $ 1,257 $ 29,795 $ 725 $ 656 $ 32,433

Collaborative Arrangements

Collaborative Arrangements	6 Months Ended
	Jun. 30, 2015
Collaborative Arrangements
Collaborative Arrangements	Collaborative Arrangements Cystic Fibrosis Foundation Therapeutics Incorporated In April 2011, the Company entered into an amendment (the “April 2011 Amendment”) to its existing collaboration agreement with Cystic Fibrosis Foundation Therapeutics Incorporated (“CFFT”) pursuant to which CFFT agreed to provide financial support for (i) development activities for VX-661, a compound that targets the processing and trafficking defect of the F508del CFTR proteins discovered under the collaboration, and (ii) additional research and development activities directed at discovering new compounds targeting the processing and trafficking defect of the F508del protein. Under the April 2011 Amendment, CFFT agreed to provide the Company with up to $75.0 million in funding over approximately five years for research and development activities. The Company retains the right to develop and commercialize KALYDECO (ivacaftor), ORKAMBI (lumacaftor in combination with ivacaftor), lumacaftor, VX-661 and any other compounds discovered during the course of the research collaboration with CFFT. The Company recognized no collaborative revenues from this collaboration during the three and six months ended June 30, 2015 and $1.6 million and $4.5 million of collaborative revenues from this collaboration during the three and six months ended June 30, 2014 , respectively. In the original agreement, as amended prior to the April 2011 Amendment, the Company agreed to pay CFFT tiered royalties calculated as a percentage, ranging from single digits to sub-teens, of annual net sales of any approved drugs discovered during the research term that ended in 2008, including KALYDECO, ORKAMBI, lumacaftor and VX-661. The April 2011 Amendment provides for a tiered royalty in the same range on net sales of compounds targeting the processing and trafficking defect of F508del CFTR proteins discovered during the research term that began in 2011 and ended in February 2014. In each of the third quarter of 2012 and the first quarter of 2013, CFFT earned a commercial milestone payment of $9.3 million from the Company upon achievement of certain sales levels for KALYDECO. These milestones were reflected in the Company's cost of product revenues. There are no additional commercial milestone payments payable by the Company to CFFT related to sales levels for KALYDECO. The Company also is obligated to make up to two one-time commercial milestone payments to CFFT upon achievement of certain sales levels for ORKAMBI. The Company began marketing KALYDECO in the United States and certain countries in the European Union in 2012 and began marketing ORKAMBI in the United States in July 2015. The Company has royalty obligations to CFFT for each compound commercialized pursuant to this collaboration until the expiration of patents covering that compound. The Company has patents in the United States and European Union covering the composition-of-matter of ivacaftor that expire in 2027 and 2025, respectively, subject to potential patent life extensions. The Company has patents in the United States and European Union covering the composition-of-matter of lumacaftor that expire in 2030 and 2026, respectively, subject to potential patent life extensions. CFFT may terminate its funding obligations under the collaboration, as amended, in certain circumstances, in which case there will be a proportional adjustment to the royalty rates and commercial milestone payments for certain compounds. The collaboration also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Janssen Pharmaceutica NV The Company has a collaboration agreement (the “Janssen HCV Agreement”) with Janssen Pharmaceutica NV (“Janssen NV”) for the development, manufacture and commercialization of telaprevir, which Janssen NV began marketing under the brand name INCIVO in certain of its territories in September 2011. Pursuant to the Janssen HCV Agreement, as amended, Janssen NV has a fully-paid license to manufacture and commercialize INCIVO in its territories including Europe, South America, the Middle East, Africa and Australia, subject to the payment of third-party royalties on net sales of INCIVO. In addition to the collaborative revenues, the Company recorded royalty revenues and corresponding royalty expenses related to third-party royalties that Janssen NV remains responsible for based on INCIVO net sales. During the three and six months ended June 30, 2015 and 2014 , the Company recognized the following revenues attributable to the Janssen NV collaboration: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Royalty revenues (INCIVO) $ 59 $ 5,698 $ 1,584 $ 10,633 Collaborative revenues (telaprevir) 537 1,483 1,179 2,872 Total revenues attributable to the Janssen NV collaboration $ 596 $ 7,181 $ 2,763 $ 13,505 Variable Interest Entities The Company has entered into several agreements pursuant to which it has licensed rights to certain drug candidates from third-party collaborators, which has resulted in the consolidation of the third parties' financial statements into the Company's condensed consolidated financial statements as VIEs. In order to account for the fair value of the contingent milestone and royalty payments related to these collaborations under GAAP, the Company uses present-value models based on assumptions regarding the probability of achieving the relevant milestones, estimates regarding the time to develop the drug candidates, estimates of future product sales and the appropriate discount rates. The Company bases its estimate of the probability of achieving the relevant milestones on industry data for similar assets and its own experience. The discount rates used in the valuation model represent a measure of credit risk and market risk associated with settling the liabilities. Significant judgment is used in determining the appropriateness of these assumptions at each reporting period. Changes in these assumptions could have a material effect on the fair value of the contingent milestone and royalty payments. The following collaborations are, or were previously, reflected in the Company's financial statements for being consolidated as VIEs: Parion Sciences, Inc. License and Collaboration Agreement On June 4, 2015, the Company entered into a strategic collaboration and license agreement (the "Parion Agreement") with Parion Sciences, Inc. (“Parion”). Pursuant to the agreement, the Company is collaborating with Parion to develop investigational epithelial sodium channel (“ENaC”) inhibitors, including VX-371 (formerly P-1037) and P-1055, for the potential treatment of cystic fibrosis, or CF, and other pulmonary diseases. The Company is leading development activities for VX-371 and P-1055 in CF and other pulmonary diseases and is responsible for all costs, subject to certain exceptions, related to development and commercialization of the compounds. Pursuant to the Parion Agreement, the Company has worldwide development and commercial rights to Parion’s lead investigational ENaC inhibitors, VX-371 and P-1055, for the potential treatment of CF and all other pulmonary diseases and has the option to select additional compounds discovered in Parion’s research program. Parion received an $80.0 million up-front payment and has the potential to receive up to an additional (i) $490.0 million in development and regulatory milestone payments for development of ENaC inhibitors in CF, including $360.0 million related to global filing and approval milestones, (ii) $370.0 million in development and regulatory milestones for VX-371 and P-1055 in non-CF pulmonary indications and (iii) $230.0 million in development and regulatory milestones should the Company elect to develop an additional ENaC inhibitor from Parion’s research program. The Company has agreed to pay Parion tiered royalties that range from the low double digits to mid-teens as a percentage of potential sales of licensed products. The Company may terminate the Parion Agreement upon 90 days’ notice to Parion prior to any licensed product receiving marketing approval or upon 180 days’ notice after such point. Parion may terminate upon 30 days’ notice if the Comapny experiences a change of control prior to the initiation of the first Phase 3 clinical trial for a licensed product, subject to the Company's right to receive specified royalties on any subsequent commercialization of licensed products. The Parion Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the agreement will continue in effect until the expiration of the Company's royalty obligations, which expire on a country-by-country basis on the later of (i) the date the last-to-expire patent covering a licensed product expires or (ii) ten years after the first commercial sale in the country. The Company determined that Parion is a VIE based on, among other factors, the significance to Parion of the ENaC inhibitors licensed to the Company pursuant to the Parion Agreement and on the Company's power to direct the activities that most significantly impact the economic performance of Parion. Accordingly, the Company consolidated Parion's financial statements beginning on June 4, 2015. However, the Company's interests in Parion are limited to those accorded to the Company in the Parion Agreement. In particular, the Company did not acquire any equity interest in Parion, any interest in Parion's cash and cash equivalents or any control over Parion's activities that do not relate to the Parion Agreement. Consideration for the Parion Agreement The Company determined that the fair value of the consideration from the Company to Parion was $255.3 million as of June 4, 2015, which consisted of (i) an $80.0 million up-front payment, (ii) the estimated fair value of the contingent research and development milestones potentially payable by the Company to Parion and (iii) the estimated fair value of potential royalty payments payable by the Company to Parion. The Company valued the contingent milestone and royalty payments using (a) discount rates ranging from 4.1% to 5.9% for the development milestones and (b) a discount rate of 6.6% for royalties. The consideration paid and the preliminary fair value of the contingent milestone and royalty payments payable by the Company pursuant to the agreement are set forth in the table below: June 4, 2015 (in thousands) Up-front payment $ 80,000 Fair value of contingent milestone and royalty payments 175,340 Total $ 255,340 Preliminary Allocation of Assets and Liabilities For the purposes of the condensed consolidated balance sheets at June 4, 2015 and June 30, 2015, the Company preliminarily allocated the total consideration, which is comprised of the up-front payment and the fair value of the contingent milestone and royalty payments, intangible assets, goodwill, deferred tax liability, net and net other assets and liabilities. The Company recorded $255.3 million of intangible assets on the Company's condensed consolidated balance sheet for Parion's in-process research and development assets. These in-process research and development assets relate to Parion's pulmonary ENaC platform, including the intellectual property related to VX-371 and P-1055, that are licensed by the Company from Parion. The difference between the preliminary fair value of the consideration and the fair value of Parion's assets (including the fair value of intangible assets) and liabilities was allocated to goodwill. The following table summarizes the preliminary fair values of the assets and liabilities recorded on the effective date of the agreement: June 4, 2015 (in thousands) Intangible assets $ 255,340 Goodwill 10,468 Deferred tax liability (91,023 ) Net other assets (liabilities) (10,468 ) Net assets attributable to noncontrolling interests $ 164,317 BioAxone Biosciences, Inc. In October 2014, the Company entered into a license and collaboration agreement (the “BioAxone Agreement”) with BioAxone Biosciences, Inc. (“BioAxone”), a privately-held biotechnology company, which resulted in the consolidation of BioAxone as a VIE beginning on October 1, 2014. The Company paid BioAxone initial payments of $10.0 million in the fourth quarter of 2014. BioAxone has the potential to receive up to $90.0 million in milestones and fees, including development, regulatory and milestone payments and a license continuation fee. In addition, BioAxone would receive royalties and commercial milestones on future net product sales of VX-210, if any. The Company holds an option to purchase BioAxone at a predetermined price. The option expires on the earliest of (a) the day the FDA accepts the Biologics License Application submission for VX-210, (b) the day the Company elects to continue the license instead of exercising the option to purchase BioAxone and (c) March 15, 2018, subject to the Company’s option to extend this date by one year. Alios BioPharma, Inc. In 2011, the Company entered into a license and collaboration agreement (the “Alios Agreement”) with Alios BioPharma, Inc. (“Alios”), a privately-held biotechnology company, which resulted in the consolidation of Alios as a VIE through December 31, 2013. Pursuant to the Alios Agreement, the Company and Alios collaborated on the research, development and commercialization of HCV nucleotide analogues discovered by Alios through April 2014. In December 2014, the Alios Agreement terminated in accordance with its terms pursuant to a termination notice delivered by the Company in October 2014. As of September 30, 2014, the Company concluded that it no longer had significant continuing involvement with Alios due to its intent and ability to terminate the Alios Agreement, among other factors; therefore, the operations of Alios are presented as discontinued operations in these condensed consolidated financial statements . Aggregate VIE Financial Information The Company did not have any consolidated VIEs for the three and six months ended June 30, 2014. An aggregate summary of net loss attributable to noncontrolling interest related to the Company's VIEs for the three and six months ended June 30, 2015 is as follows: Three Months Ended June 30, 2015 Six Months Ended June 30, 2015 (in thousands) Loss attributable to noncontrolling interest before provision for income taxes $ (1,293 ) $ (1,579 ) Income tax provision (29,653 ) (29,590 ) Decrease in fair value of contingent milestone and royalty payments (1,198 ) (1,073 ) Net loss attributable to noncontrolling interest $ (32,144 ) $ (32,242 ) During the three and six months ended June 30, 2015 , the fair value of the contingent milestone and royalty payments related to the BioAxone collaboration increased by $0.4 million and $0.5 million , respectively. During the three months ended June 30, 2015 , the fair value of the contingent milestone and royalty payments related to the Parion collaboration decreased by $1.6 million . The changes in the fair value of the contingent milestone and royalty payments was primarily due to the changes in market interest rates. As of June 30, 2015 , the fair value of the contingent milestone and royalty payments related to the BioAxone collaboration and the Parion collaboration was $27.6 million and $173.7 million , respectively. The following summarizes items related to the Company's VIEs included in the Company's condensed consolidated balance sheets as of the dates set forth in the table: June 30, 2015 December 31, 2014 (in thousands) Restricted cash and cash equivalents (VIE) $ 88,318 $ 8,418 Prepaid expenses and other current assets 895 268 Intangible assets 284,340 29,000 Goodwill 19,391 8,923 Other assets 508 42 Accounts payable 823 189 Accrued expenses and other current liabilities 34,254 3,891 Deferred tax liability, net 108,913 11,544 Other liabilities 6,068 300 Noncontrolling interest 153,252 21,177 The Company has recorded the VIEs' cash and cash equivalents as restricted cash and cash equivalents (VIE) because (i) the Company does not have any interest in or control over the VIEs' cash and cash equivalents and (ii) the Company's agreements with each VIE do not provide for the VIEs' cash and cash equivalents to be used for the development of the assets that the Company licensed from the applicable VIE. Assets recorded as a result of consolidating our VIEs' financial condition into the Company's balance sheet do not represent additional assets that could be used to satisfy claims against the Company's general assets. Outlicense Arrangements In the ordinary course of the Company's business, the Company has entered into various agreements pursuant to which it has outlicensed rights to certain drug candidates to third-party collaborators. Although the Company does not consider any of these outlicense arrangements to be material, the most notable of these outlicense arrangements is described below. Pursuant to these outlicense arrangements, our collaborators are responsible for all costs related to the continued development of such drug candidates. Depending on the terms of the arrangements, the Company's collaborators may be required to make upfront payments, milestone payments upon the achievement of certain product research and development objectives and/or pay royalties on future sales, if any, of commercial products resulting from the collaboration. Janssen Pharmaceuticals, Inc. In June 2014, the Company entered into an agreement (the “Janssen Influenza Agreement”) with Janssen Pharmaceuticals, Inc. (“Janssen Inc.”), which was amended in October 2014 to clarify certain roles and responsibilities of the parties. Pursuant to the Janssen Influenza Agreement, Janssen Inc. has an exclusive worldwide license to develop and commercialize certain drug candidates for the treatment of influenza, including VX-787. The Company received non-refundable payments of $35.0 million from Janssen Inc. in 2014, which were recorded as collaborative revenue. The Company has the potential to receive development, regulatory and commercial milestone payments as well as royalties on future product sales, if any. Janssen Inc. is responsible for costs related to the development and commercialization of the compounds. During the three and six months ended June 30, 2015 , the Company recorded reimbursement for these development activities of $7.1 million and $14.7 million , respectively. During the three and six months ended June 30, 2014 , the Company recorded no reimbursement for these development activities. The reimbursements are recorded as a reduction to development expense in the Company's condensed consolidated statements of operations primarily due to the fact that Janssen Inc. directs the activities and selects the suppliers associated with these activities. Janssen Inc. may terminate the Janssen Influenza Agreement, subject to certain exceptions, upon six months' notice.

Earnings Per Share

Earnings Per Share	6 Months Ended
	Jun. 30, 2015
Earnings Per Share [Abstract]
Earnings Per Share	Earnings Per Share Basic net loss per share attributable to Vertex common shareholders is based upon the weighted-average number of common shares outstanding during the period, excluding restricted stock and restricted stock units that have been issued but are not yet vested. Diluted net loss per share attributable to Vertex common shareholders is based upon the weighted-average number of common shares outstanding during the period plus additional weighted-average common equivalent shares outstanding during the period when the effect is dilutive. The Company did not include the securities described in the following table in the computation of the net loss from continuing operations per share attributable to Vertex common shareholder calculations because the effect would have been anti-dilutive during each period: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Stock options 11,933 14,549 11,933 14,549 Unvested restricted stock and restricted stock units 3,355 2,584 3,355 2,584

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2015
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The fair value of the Company’s financial assets and liabilities reflects the Company’s estimate of amounts that it would have received in connection with the sale of the assets or paid in connection with the transfer of the liabilities in an orderly transaction between market participants at the measurement date. In connection with measuring the fair value of its assets and liabilities, the Company seeks to maximize the use of observable inputs (market data obtained from sources independent from the Company) and to minimize the use of unobservable inputs (the Company’s assumptions about how market participants would price assets and liabilities). The following fair value hierarchy is used to classify assets and liabilities based on the observable inputs and unobservable inputs used in order to value the assets and liabilities: Level 1: Quoted prices in active markets for identical assets or liabilities. An active market for an asset or liability is a market in which transactions for the asset or liability occur with sufficient frequency and volume to provide pricing information on an ongoing basis. Level 2: Observable inputs other than Level 1 inputs. Examples of Level 2 inputs include quoted prices in active markets for similar assets or liabilities and quoted prices for identical assets or liabilities in markets that are not active. Level 3: Unobservable inputs based on the Company’s assessment of the assumptions that market participants would use in pricing the asset or liability. The Company’s investment strategy is focused on capital preservation. The Company invests in instruments that meet the credit quality standards outlined in the Company’s investment policy. This policy also limits the amount of credit exposure to any one issue or type of instrument. As of June 30, 2015 , the Company’s investments were in money market funds, corporate debt securities and commercial paper. As of June 30, 2015 , all of the Company’s financial assets that were subject to fair value measurements were valued using observable inputs. The Company’s financial assets valued based on Level 1 inputs consisted of money market funds. The Company’s financial assets valued based on Level 2 inputs consisted of corporate debt securities and commercial paper, which consist of investments in highly-rated investment-grade corporations. The following table sets forth the Company’s financial assets and liabilities subject to fair value measurements: Fair Value Measurements as of June 30, 2015 Fair Value Hierarchy Total Level 1 Level 2 Level 3 (in thousands) Financial assets carried at fair value: Cash equivalents: Money market funds $ 518,084 $ 518,084 $ — $ — Marketable securities: Corporate debt securities 120,408 — 120,408 — Commercial paper 25,499 — 25,499 — Prepaid and other current assets: Foreign currency forward contracts 1,087 — 1,087 — Total financial assets $ 665,078 $ 518,084 $ 146,994 $ — Financial liabilities carried at fair value: Other liabilities, current portion: Foreign currency forward contracts $ (2,737 ) $ — $ (2,737 ) $ — Other liabilities, excluding current portion: Foreign currency forward contracts (313 ) — (313 ) — Total financial liabilities $ (3,050 ) $ — $ (3,050 ) $ — The Company's VIEs invested in cash equivalents consisting of money market funds of $84.4 million as of June 30, 2015 , which are valued based on Level 1 inputs. These cash equivalents are not included in the table above. The Company’s noncontrolling interest related to VIEs includes the fair value of the contingent milestone and royalty payments , which are valued based on Level 3 inputs. Please refer to Note C, “Collaborative Arrangements,” for further information. As of June 30, 2015 , the fair value and carrying value of the Company's Term Loan was $294.8 million . The fair value of the Company's Term Loan was estimated based on Level 3 inputs computed using the effective interest rate of the Term Loan. The effective interest rate considers the timing and amount of estimated future interest payments. Please refer to Note K, "Long-term Obligations" for further information regarding the Company's Term Loan.

Marketable Securities

Marketable Securities	6 Months Ended
	Jun. 30, 2015
Cash and Cash Equivalents [Abstract]
Marketable Securities	Marketable Securities A summary of the Company’s cash, cash equivalents and marketable securities is shown below: Amortized Cost Gross Gross Fair Value (in thousands) As of June 30, 2015 Cash and cash equivalents: Cash and money market funds $ 870,543 $ — $ — $ 870,543 Total cash and cash equivalents $ 870,543 $ — $ — $ 870,543 Marketable securities: Commercial paper (due within 1 year) $ 25,470 $ 29 $ — $ 25,499 Corporate debt securities (due within 1 year) 120,430 12 (34 ) 120,408 Total marketable securities $ 145,900 $ 41 $ (34 ) $ 145,907 Total cash, cash equivalents and marketable securities $ 1,016,443 $ 41 $ (34 ) $ 1,016,450 As of December 31, 2014 Cash and cash equivalents: Cash and money market funds $ 625,259 $ — $ — $ 625,259 Total cash and cash equivalents $ 625,259 $ — $ — $ 625,259 Marketable securities: Government-sponsored enterprise securities (due within 1 year) $ 463,788 $ 14 $ (52 ) $ 463,750 Commercial paper (due within 1 year) 51,674 72 — 51,746 Corporate debt securities (due within 1 year) 196,065 2 (66 ) 196,001 Corporate debt securities (due after 1 year through 5 years) 50,443 — (93 ) 50,350 Total marketable securities $ 761,970 $ 88 $ (211 ) $ 761,847 Total cash, cash equivalents and marketable securities $ 1,387,229 $ 88 $ (211 ) $ 1,387,106 The Company has a limited number of marketable securities in insignificant loss positions as of June 30, 2015 , which the Company does not intend to sell and has concluded it will not be required to sell before recovery of the amortized costs for the investment at maturity. There were no charges recorded for other-than-temporary declines in fair value of marketable securities nor gross realized gains or losses recognized in the three and six months ended June 30, 2015 and 2014 .

Accumulated Other Comprehensive

Accumulated Other Comprehensive Income (Loss)	6 Months Ended
	Jun. 30, 2015
Equity [Abstract]
Accumulated Other Comprehensive Income (Loss)	Accumulated Other Comprehensive (Loss) Income A summary of the Company's changes in accumulated other comprehensive (loss) income by component is shown below: Foreign Currency Translation Adjustment Unrealized Holding Gains (Losses) on Marketable Securities Unrealized Gains (Losses) on Foreign Currency Forward Contracts Total (in thousands) Balance at December 31, 2014 $ (971 ) $ (123 ) $ 2,011 $ 917 Other comprehensive (loss) income before reclassifications 1,220 130 (1,370 ) (20 ) Amounts reclassified from accumulated other comprehensive loss — — (2,604 ) (2,604 ) Net current period other comprehensive (loss) income $ 1,220 $ 130 $ (3,974 ) $ (2,624 ) Balance at June 30, 2015 $ 249 $ 7 $ (1,963 ) $ (1,707 ) Foreign Currency Translation Adjustment Unrealized Holding Gains on Marketable Securities Unrealized Losses on Foreign Currency Forward Contracts Total (in thousands) Balance at December 31, 2013 $ (325 ) $ 42 $ (23 ) $ (306 ) Other comprehensive income (loss) before reclassifications 353 55 (108 ) 300 Amounts reclassified from accumulated other comprehensive loss — — (17 ) (17 ) Net current period other comprehensive income (loss) $ 353 $ 55 $ (125 ) $ 283 Balance at June 30, 2014 $ 28 $ 97 $ (148 ) $ (23 )

Hedging

Hedging	6 Months Ended
	Jun. 30, 2015
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Hedging	Hedging The Company maintains a hedging program intended to mitigate the effect of changes in foreign exchange rates for a portion of the Company’s forecasted product revenues denominated in certain foreign currencies. The program includes foreign currency forward contracts that are designated as cash flow hedges under GAAP having contractual durations from one to eighteen months. To date, the existence of operational sites in countries outside the United States has decreased the degree to which the Company has sought to hedge its revenues in certain foreign currencies. The Company formally documents the relationship between foreign currency forward contracts (hedging instruments) and forecasted product revenues (hedged items), as well as the Company's risk management objective and strategy for undertaking various hedging activities, which includes matching all foreign currency forward contracts that are designated as cash flow hedges to forecasted transactions. The Company also formally assesses, both at the hedge’s inception and on an ongoing basis, whether the foreign currency forward contracts are highly effective in offsetting changes in cash flows of hedged items on a prospective and retrospective basis. If the Company determines that a (i) foreign currency forward contract is not highly effective as a cash flow hedge, (ii) foreign currency forward contract has ceased to be a highly effective hedge or (iii) forecasted transaction is no longer probable of occurring, the Company would discontinue hedge accounting treatment prospectively. The Company measures effectiveness based on the change in fair value of the forward contracts and the fair value of the hypothetical foreign currency forward contracts with terms that match the critical terms of the risk being hedged. As of June 30, 2015 , all hedges were determined to be highly effective and the Company has not recorded any ineffectiveness related to the hedging program. The following table summarizes the notional amount of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges: As of June 30, 2015 As of December 31, 2014 Foreign Currency (in thousands) Euro $ 102,796 $ 20,209 British pound sterling 82,960 13,515 Australian dollar 25,993 — Total foreign currency forward contracts $ 211,749 $ 33,724 The following table summarizes the fair value of the Company's outstanding foreign currency forward contracts designated as cash flow hedges under GAAP included on the Company's condensed consolidated balance sheets: As of June 30, 2015 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 1,087 Other liabilities, current portion $ (2,737 ) Other assets — Other liabilities, excluding current portion (313 ) Total assets $ 1,087 Total liabilities $ (3,050 ) As of December 31, 2014 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 2,011 Other liabilities, current portion $ — Total assets $ 2,011 Total liabilities $ — The following table summarizes the potential effect of offsetting derivatives by type of financial instrument on the Company's condensed consolidated balance sheets: As of June 30, 2015 Gross Amounts Recognized Gross Amounts Offset Gross Amount Presented Gross Amount Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 1,087 $ — $ 1,087 $ (1,087 ) $ — Total liabilities $ (3,050 ) $ — $ (3,050 ) $ 1,087 $ (1,963 ) As of December 31, 2014 Gross Amounts Recognized Gross Amounts Offset Gross Amount Presented Gross Amount Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 2,011 $ — $ 2,011 $ — $ 2,011

Inventories

Inventories	6 Months Ended
	Jun. 30, 2015
Inventory Disclosure [Abstract]
Inventories	Inventories Inventories consisted of the following: As of June 30, 2015 As of December 31, 2014 (in thousands) Raw materials $ 8,147 $ 8,506 Work-in-process 30,989 20,508 Finished goods 2,977 1,834 Total $ 42,113 $ 30,848

Intangible Assets and Goodwill

Intangible Assets and Goodwill	6 Months Ended
	Jun. 30, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible Assets and Goodwill	Intangible Assets and Goodwill Intangible Assets As of June 30, 2015 , in-process research and development intangible assets of $284.3 million were recorded on the Company's condensed consolidated balance sheet. The increase of $255.3 million as compared to the $29.0 million recorded as of December 31, 2014 is due to the Company's collaboration with Parion. In June 2015, in connection with entering into the Parion Agreement, the Company recorded an in-process research and development intangible asset of $255.3 million based on the Company’s estimate of the fair value of Parion’s lead investigational ENaC inhibitors, including VX-371 and P-1055, that were licensed by the Company from Parion. The Company aggregated the fair value of the ENaC inhibitors into a single intangible asset because the phase, nature and risks of development as well as the amount and timing of benefits associated with the assets were similar. In October 2014, the Company recorded an in-process research and development intangible asset of $29.0 million based on the Company’s estimate of the fair value of VX-210, a drug candidate for patients with spinal cord injuries that was licensed by the Company from BioAxone. The Company used discount rates of 7.1% and 7.5% in the present-value models to estimate the fair values of the ENaC inhibitors and VX-210 intangible assets, respectively. The Company also conducted an evaluation of Parion and BioAxone's other programs at the effective date of the Parion Agreement and BioAxone Agreement, respectively, and determined that market participants would not have ascribed value to those programs because of the stage of development of the assets in each program and uncertainties related to the potential clinical development and commercialization of the programs. Goodwill As of June 30, 2015 , goodwill of $50.4 million was recorded on the Company's condensed consolidated balance sheet. The Company allocated $10.5 million to goodwill related to the Parion Agreement during the six months ended June 30, 2015 . This goodwill relates to the potential synergies between licensed drug candidates and the Company's CF drugs and drug candidates. None of the goodwill related to the Parion Agreement is expected to be deductible for income tax purposes. As of December 31, 2014 , $39.9 million of goodwill was recorded on the Company’s consolidated balance sheet.

Long-term Obligations

Long-term Obligations	6 Months Ended
	Jun. 30, 2015
Long-term Debt and Capital Lease Obligations [Abstract]
Long-term Obligations	Long-term Obligations Fan Pier Leases In 2011, the Company entered into two lease agreements, pursuant to which the Company leases approximately 1.1 million square feet of office and laboratory space in two buildings (the “Buildings”) at Fan Pier in Boston, Massachusetts (the “Fan Pier Leases”). The Company commenced lease payments in December 2013, and will make lease payments pursuant to the Fan Pier Leases through December 2028. The Company has an option to extend the term of the Fan Pier Leases for an additional ten years . Because the Company was involved in the construction project and determined that the Fan Pier Leases did not meet the criteria for “sale-leaseback” treatment upon completion of the Buildings, the Company recorded project construction costs incurred by the landlord as an asset and a related financing obligation during the construction period and began depreciating the asset and incurring interest expense related to the financing obligation in 2013. The Company bifurcates its lease payments pursuant to the Fan Pier Leases into (i) a portion that is allocated to the Buildings and (ii) a portion that is allocated to the land on which the Buildings were constructed. The portion of the lease obligations allocated to the land is treated as an operating lease that commenced in 2011. Property and equipment, net, included $508.9 million and $515.0 million as of June 30, 2015 and December 31, 2014 , respectively, related to construction costs for the Buildings. The carrying value of the Company's lease agreement liability for the Buildings was $473.2 million and $473.4 million as of June 30, 2015 and December 31, 2014 , respectively. Term Loan On July 9, 2014, the Company entered into a credit agreement with the lenders party thereto, and Macquarie US Trading LLC ("Macquarie"), as administrative agent. The credit agreement provides for a $300.0 million senior secured term loan ("Term Loan"). The credit agreement also provides that, subject to satisfaction of certain conditions, the Company may request that the lenders establish an incremental senior secured term loan facility in an aggregate amount not to exceed $200.0 million . The Term Loan initially bore interest at a rate of 7.2% per annum, which will be reduced to 6.2% per annum based on the FDA's approval of ORKAMBI. The Term Loan will bear interest at a rate of LIBOR plus 5.0% per annum during the third year of the term. The maturity date of all loans under the facilities is July 9, 2017. Interest is payable quarterly and on the maturity date. The Company is required to repay principal on the Term Loan in installments of $15.0 million per quarter from October 1, 2015 through July 1, 2016 and in installments of $60.0 million per quarter from October 1, 2016 through the maturity date. The Company may prepay the Term Loan, in whole or in part, at any time; provided that prepayments prior to the July 9, 2016 are subject to a make-whole premium to ensure Macquarie receives approximately the present value of two years of interest payments over the life of the loan. The Company's obligations under the facilities are unconditionally guaranteed by certain of its domestic subsidiaries. All obligations under the facilities, and the guarantees of those obligations, are secured, subject to certain exceptions, by substantially all of the Company's assets and the assets of all guarantors, including the pledge of all or a portion of the equity interests of certain of its subsidiaries. The credit agreement requires that the Company maintain, on a quarterly basis, a minimum level of KALYDECO net revenues. Further, the credit agreement includes negative covenants, subject to exceptions, restricting or limiting the Company's ability and the ability of its subsidiaries to, among other things, incur additional indebtedness, grant liens, engage in certain investment, acquisition and disposition transactions, pay dividends, repurchase capital stock and enter into transactions with affiliates. The credit agreement also contains customary representations and warranties, affirmative covenants and events of default, including payment defaults, breach of representations and warranties, covenant defaults and cross defaults. If an event of default occurs, the administrative agent would be entitled to take various actions, including the acceleration of amounts due under outstanding loans. There have been no events of default as of or during the period ended June 30, 2015 . Based on the Company's evaluation of the Term Loan, the Company determined that the Term Loan contains several embedded derivatives. These embedded derivatives are clearly and closely related to the host instrument because they relate to the Company's credit risk; therefore, they do not require bifurcation from the host instrument, the Term Loan. The Company incurred $5.3 million in fees paid to Macquarie that were recorded as a discount on the Term Loan and are being recorded as interest expense using the effective interest method over the term of the loan in the Company’s condensed consolidated statements of operations . As of June 30, 2015 , the unamortized discount associated with the Term Loan that was embedded in the senior secured term loan caption on the Company’s condensed consolidated balance sheet was $5.2 million .

Stock-based Compensation Expens

Stock-based Compensation Expense	6 Months Ended
	Jun. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-based Compensation Expense	Stock-based Compensation Expense The Company issues stock options, restricted stock and restricted stock units with service conditions, which are generally the vesting periods of the awards. The Company also has issued, to certain members of senior management, restricted stock and restricted stock units that vest upon the earlier of the satisfaction of (i) a performance condition or (ii) a service condition and stock options that vest upon the earlier of the satisfaction of (a) performance conditions or (b) a service condition. In addition, the Company issued pursuant to a retention program restricted stock awards to certain members of senior management that will vest upon the satisfaction of both (i) a performance condition and (ii) a service condition. The Company also issues shares pursuant to an employee stock purchase plan ("ESPP"). In the second quarter of 2015, the Company’s shareholders approved an amendment and restatement of the 2013 Stock and Option Plan that, among other things, increased the number of shares of common stock available for issuance under the plan by 7,800,000 shares, plus the number of shares that remained available for issuance under our 2006 Stock and Option Plan, which rolled-over into the 2013 Stock and Option Plan. During the three and six months ended June 30, 2015 and 2014 , the Company recognized the following stock-based compensation expense included in loss from continuing operations: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Stock-based compensation expense by type of award: Stock options $ 37,687 $ 26,985 $ 66,646 $ 52,112 Restricted stock and restricted stock units 24,902 14,020 52,071 33,013 ESPP share issuances 1,825 1,681 3,965 4,348 Less stock-based compensation expense capitalized to inventories (1,153 ) (242 ) (2,037 ) (449 ) Total stock-based compensation included in costs and expenses $ 63,261 $ 42,444 $ 120,645 $ 89,024 Stock-based compensation expense by line item: Research and development expenses $ 41,632 $ 27,253 $ 79,849 $ 60,153 Sales, general and administrative expenses 21,629 15,191 40,796 28,871 Total stock-based compensation included in costs and expenses $ 63,261 $ 42,444 $ 120,645 $ 89,024 The following table sets forth the Company's unrecognized stock-based compensation expense, net of estimated forfeitures, by type of award and the weighted-average period over which that expense is expected to be recognized: As of June 30, 2015 Unrecognized Expense, Weighted-average (in thousands) (in years) Type of award: Stock options $ 169,671 2.22 Restricted stock and restricted stock units $ 175,285 2.73 ESPP share issuances $ 3,953 0.59 The following table summarizes information about stock options outstanding and exercisable at June 30, 2015 : Options Outstanding Options Exercisable Range of Exercise Prices Number Weighted-average Weighted-average Number Weighted-average (in thousands) (in years) (per share) (in thousands) (per share) $17.16–$20.00 147 2.52 $ 18.87 147 $ 18.87 $20.01–$40.00 2,888 4.04 $ 34.82 2,534 $ 34.60 $40.01–$60.00 3,015 7.12 $ 48.32 1,534 $ 49.67 $60.01–$80.00 1,705 8.60 $ 75.99 539 $ 74.93 $80.01–$100.00 2,108 8.57 $ 90.22 621 $ 86.72 $100.01–$120.00 1,868 9.58 $ 109.24 113 $ 109.25 $120.01–$127.54 202 9.92 $ 127.31 165 $ 127.54 Total 11,933 7.22 $ 66.92 5,653 $ 52.06

Other Arrangements

Other Arrangements	6 Months Ended
	Jun. 30, 2015
Other Income and Expenses [Abstract]
Other Arrangements	Other Arrangements Sale of HIV Protease Inhibitor Royalty Stream In 2008, the Company sold to a third party its rights to receive royalty payments from GlaxoSmithKline plc, net of royalty amounts to be earned by and due to a third party, for a one-time cash payment of $160.0 million . These royalty payments relate to net sales of HIV protease inhibitors, which had been developed pursuant to a collaboration agreement between the Company and GlaxoSmithKline plc. As of June 30, 2015 , the Company had $35.4 million in deferred revenues related to the one-time cash payment, which it is recognizing over the life of the collaboration agreement with GlaxoSmithKline plc based on the units-of-revenue method. In addition, the Company continues to recognize royalty revenues equal to the amount of the third-party subroyalty and an offsetting royalty expense for the third-party subroyalty payment. Other income (expense), net In April 2014, the Company received a one-time cash payment of $36.7 million from its landlord pursuant to the Fan Pier Leases. This payment related to bonds issued pursuant to an Infrastructure Development Assistance Agreement between The Commonwealth of Massachusetts and the Company’s landlord. The bonds were issued in connection with the landlord’s contribution to infrastructure improvements and also were dependent upon employment levels at the Company through the bond issuance date. The Company accounted for the cash payment as a government grant as it was provided in part related to the Company’s employment level in Massachusetts. Such grants are recognized as income in the period in which the conditions of the grant are met and there is reasonable assurance that the grant will be received, provided it is not subject to refund. In the second quarter of 2014, the Company recorded $36.7 million as a credit to other income (expense), net in its consolidated statements of operations because the Company’s employment obligations related to these funds were satisfied as of the date of issuance of the bonds and the payment received was not subject to refund.

Income Taxes

Income Taxes	6 Months Ended
	Jun. 30, 2015
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company is subject to U.S. federal, state, and foreign income taxes. For the three and six months ended June 30, 2015 , the Company recorded a provision for income taxes of $30.1 million and $30.4 million , respectively. The provision for income taxes recorded in the three and six months ended June 30, 2015 included $29.7 million related to the estimated income tax effect on Parion of the Company's $80.0 million up-front payment to Parion in June 2015. The Company has no liability for taxes payable by Parion and the income tax provision and related liability have been allocated to noncontrolling interest (VIE). For the three and six months ended June 30, 2014 , the Company recorded a provision for income taxes of $0.7 million and $1.5 million , respectively, related to state income taxes and income earned in various foreign jurisdictions. As of June 30, 2015 and December 31, 2014 , the Company had unrecognized tax benefits of $0.9 million . The Company recognizes interest and penalties related to income taxes as a component of income tax expense. As of June 30, 2015 , no interest and penalties have been accrued. The Company does not expect that its unrecognized tax benefits will materially increase within the next twelve months. The Company did not recognize any material interest or penalties related to uncertain tax positions as of June 30, 2015 and December 31, 2014 . In 2015, it is reasonably possible that the Company will reduce the balance of its unrecognized tax benefits by approximately $0.5 million due to the application of statute of limitations and settlements with taxing authorities, all of which would reduce the Company’s effective tax rate. The Company continues to maintain a valuation allowance against certain deferred tax assets where it is more likely than not that the deferred tax asset will not be realized because of its extended history of annual losses. The Company files U.S. federal income tax returns and income tax returns in various state, local and foreign jurisdictions. The Company is no longer subject to any tax assessment from an income tax examination in the United States before 2010 or any other major taxing jurisdiction for years before 2009, except where the Company has net operating losses or tax credit carryforwards that originated before 2009. The Company currently is under examination by the Internal Revenue Service, Pennsylvania, Delaware, New York and Texas for the year ended December 31, 2011. No adjustments have been reported. The Company is not under examination by any other jurisdictions for any tax year. The Company concluded audits with Massachusetts and Revenue Quebec during 2015 and the Canada Revenue Agency and Revenue Quebec during 2014 with no material adjustments. The Company currently intends to reinvest the total amount of its unremitted earnings. At June 30, 2015 , foreign earnings, which were not significant, have been retained indefinitely by foreign subsidiary companies for reinvestment; therefore, no provision has been made for income taxes that would be payable upon the distribution of such earnings, and it would not be practicable to determine the amount of the related unrecognized deferred income tax liability. Upon repatriation of those earnings, in the form of dividends or otherwise, the Company would be subject to U.S. federal income taxes (subject to an adjustment for foreign tax credits) and withholding taxes payable to the various foreign countries.

Restructuring Liabilities

Restructuring Liabilities	6 Months Ended
	Jun. 30, 2015
Restructuring and Related Activities [Abstract]
Restructuring Liabilities	Restructuring Liabilities 2003 Kendall Restructuring In 2003, the Company adopted a plan to restructure its operations to coincide with its increasing internal emphasis on advancing drug candidates through clinical development to commercialization. The restructuring liability relates to specialized laboratory and office space that is leased to the Company pursuant to a 15 -year lease that terminates in 2018. The Company has not used more than 50% of this space since it adopted the plan to restructure its operations in 2003. This unused laboratory and office space currently is subleased to third parties. The activities related to the restructuring liability for the three and six months ended June 30, 2015 and 2014 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Liability, beginning of the period $ 9,506 $ 18,324 $ 11,596 $ 19,115 Cash payments (2,584 ) (3,960 ) (6,569 ) (7,822 ) Cash received from subleases 2,799 2,689 5,275 5,378 Restructuring expense (income) 203 (2,117 ) (378 ) (1,735 ) Liability, end of the period $ 9,924 $ 14,936 $ 9,924 $ 14,936 Fan Pier Move Restructuring In connection with the relocation of its Massachusetts operations to Fan Pier in Boston, Massachusetts, which commenced in 2013, the Company is incurring restructuring charges related to its remaining lease obligations at its facilities in Cambridge, Massachusetts. The majority of these restructuring charges were recorded in the third quarter of 2014 upon decommissioning three facilities in Cambridge. During the first quarter of 2015, the Company terminated two of these lease agreements resulting in a credit to restructuring expense equal to the difference between the Company’s estimated future cash flows related to its lease obligations for these facilities and the termination payment paid to the Company’s landlord on the effective date of the termination. The third major facility included in this restructuring activity is 120,000 square feet of the Kendall Square Facility that the Company continued to use for its operations following its 2003 Kendall Restructuring . The rentable square footage in this portion of the Kendall Square Facility was subleased to a third party in February 2015. The Company will continue to incur charges through April 2018 related to the difference between the Company’s estimated future cash flows related to this portion of the Kendall Square Facility , which include an estimate for sublease income to be received from the Company's sublessee and its actual cash flows. The Company discounted the estimated cash flows related to this restructuring activity at a discount rate of 9% . The activities related to the restructuring liability for the three and six months ended June 30, 2015 and 2014 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Liability, beginning of the period $ 11,137 $ 3,722 $ 33,390 $ 797 Cash payments (3,095 ) (2,143 ) (22,351 ) (4,377 ) Restructuring expense (income) 975 1,677 (2,022 ) 6,836 Liability, end of the period $ 9,017 $ 3,256 $ 9,017 $ 3,256 Other Restructuring Activities The Company has incurred several other restructuring activities that are unrelated to its 2003 Kendall Restructuring and the Fan Pier Move Restructuring . In October 2013, the Company adopted a restructuring plan that included (i) a workforce reduction primarily related to the commercial support of INCIVEK following the continued and rapid decline in the number of patients being treated with INCIVEK as new medicines for the treatment of HCV infection neared approval and (ii) the write-off of certain assets. This action resulted from the Company's decision to focus its investment on future opportunities in cystic fibrosis and other research and development programs. The activities related to the Company's other restructuring liabilities for the three and six months ended June 30, 2015 and 2014 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Liability, beginning of the period $ 845 $ 1,821 $ 869 $ 8,441 Cash payments (893 ) (1,199 ) (1,223 ) (8,466 ) Restructuring expense 950 170 1,256 817 Liability, end of the period $ 902 $ 792 $ 902 $ 792

Commitments and Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2015
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Financing Arrangements As of June 30, 2015 , the Company had irrevocable stand-by letters of credit outstanding that were issued in connection with property leases and other similar agreements totaling $21.9 million that are cash collateralized. The cash used to support these letters of credit is included in restricted cash, as of June 30, 2015 , on the Company's condensed consolidated balance sheet. Litigation On May 28, 2014, a purported shareholder class action Local No. 8 IBEW Retirement Plan & Trust v. Vertex Pharmaceuticals Incorporated, et al. was filed in the United States District Court for the District of Massachusetts, naming the Company and certain of the Company's current and former officers and directors as defendants. The lawsuit alleged that the Company made material misrepresentations and/or omissions of material fact in the Company's disclosures during the period from May 7, 2012 through May 29, 2012, all in violation of Section 10(b) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 promulgated thereunder. The purported class consists of all persons (excluding defendants) who purchased the Company’s common stock between May 7, 2012 and May 29, 2012. The plaintiffs seek unspecified monetary damages, costs and attorneys’ fees as well as disgorgement of the proceeds from certain individual defendants’ sales of the Company’s stock. On October 8, 2014, the Court approved Local No. 8 IBEW Retirement Fund as lead plaintiff, and Scott and Scott LLP as lead counsel for the plaintiff and the putative class. On February 23, 2015, the Company filed a reply to the plaintiffs’ opposition to its motion to dismiss. The court heard oral argument on the motion to dismiss on March 6, 2015 and took the motion under advisement. The Company believes the claims to be without merit and intends to vigorously defend the litigation. As of June 30, 2015 , the Company has not recorded any reserves for this purported class action. Guaranties and Indemnifications As permitted under Massachusetts law, the Company’s Articles of Organization and By-laws provide that the Company will indemnify certain of its officers and directors for certain claims asserted against them in connection with their service as an officer or director. The maximum potential amount of future payments that the Company could be required to make under these indemnification provisions is unlimited. However, the Company has purchased directors’ and officers’ liability insurance policies that could reduce its monetary exposure and enable it to recover a portion of any future amounts paid. No indemnification claims currently are outstanding, and the Company believes the estimated fair value of these indemnification arrangements is minimal. The Company customarily agrees in the ordinary course of its business to indemnification provisions in agreements with clinical trial investigators and sites in its drug development programs, sponsored research agreements with academic and not-for-profit institutions, various comparable agreements involving parties performing services for the Company, and its real estate leases. The Company also customarily agrees to certain indemnification provisions in its drug discovery, development and commercialization collaboration agreements. With respect to the Company’s clinical trials and sponsored research agreements, these indemnification provisions typically apply to any claim asserted against the investigator or the investigator’s institution relating to personal injury or property damage, violations of law or certain breaches of the Company’s contractual obligations arising out of the research or clinical testing of the Company’s compounds or drug candidates. With respect to lease agreements, the indemnification provisions typically apply to claims asserted against the landlord relating to personal injury or property damage caused by the Company, to violations of law by the Company or to certain breaches of the Company’s contractual obligations. The indemnification provisions appearing in the Company’s collaboration agreements are similar to those for the other agreements discussed above, but in addition provide some limited indemnification for its collaborator in the event of third-party claims alleging infringement of intellectual property rights. In each of the cases above, the indemnification obligation generally survives the termination of the agreement for some extended period, although the Company believes the obligation typically has the most relevance during the contract term and for a short period of time thereafter. The maximum potential amount of future payments that the Company could be required to make under these provisions is generally unlimited. The Company has purchased insurance policies covering personal injury, property damage and general liability that reduce its exposure for indemnification and would enable it in many cases to recover all or a portion of any future amounts paid. The Company has never paid any material amounts to defend lawsuits or settle claims related to these indemnification provisions. Accordingly, the Company believes the estimated fair value of these indemnification arrangements is minimal. Other Contingencies The Company has certain contingent liabilities that arise in the ordinary course of its business activities. The Company accrues a reserve for contingent liabilities when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. There were no material contingent liabilities accrued as of June 30, 2015 or December 31, 2014 .

Basis of Presentation and Acc25

Basis of Presentation and Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2015
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated ("Vertex" or the "Company") in accordance with accounting principles generally accepted in the United States of America ("GAAP"). The condensed consolidated financial statements reflect the operations of (i) the Company, (ii) its wholly-owned subsidiaries and (iii) consolidated variable interest entities (VIEs). All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended June 30, 2015 and 2014 . The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, 2014 , which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2014 that was filed with the Securities and Exchange Commission (the “SEC”) on February 13, 2015 (the "2014 Annual Report on Form 10-K").
Use of Estimates and Summary of Significant Accounting Policies	Use of Estimates and Summary of Significant Accounting Policies The preparation of condensed consolidated financial statements in accordance with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with the calculation of revenues, inventories, research and development expenses, stock-based compensation expense, restructuring expense, the fair value of intangible assets, goodwill, noncontrolling interest, the consolidation of VIEs, leases and the provision for or benefit from income taxes. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. The Company's significant accounting policies are described in Note A, "Nature of Business and Accounting Policies," in the 2014 Annual Report on Form 10-K.
Recent Accounting Pronouncements	Recent Accounting Pronouncements For a discussion of recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2014 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the six months ended June 30, 2015 that had a material effect on its condensed consolidated financial statements.

Product Revenues, Net (Tables)

Product Revenues, Net (Tables)	6 Months Ended
	Jun. 30, 2015
Product Revenues [Abstract]
Schedule of product revenue allowances and reserve categories	The following table summarizes activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2015 : Trade Rebates, Product Other Total (in thousands) Balance at December 31, 2014 $ 1,463 $ 29,102 $ 4,713 $ 745 $ 36,023 Provision related to current period sales 2,865 20,305 181 1,251 24,602 Adjustments related to prior period sales (86 ) (5,958 ) (975 ) (235 ) (7,254 ) Credits/payments made (2,985 ) (13,654 ) (3,194 ) (1,105 ) (20,938 ) Balance at June 30, 2015 $ 1,257 $ 29,795 $ 725 $ 656 $ 32,433

Collaborative Arrangements Coll

Collaborative Arrangements Collaborative Arrangements (Tables)	6 Months Ended
	Jun. 30, 2015
Collaborative Arrangements
Schedule of Recognized Collaborative Revenue	During the three and six months ended June 30, 2015 and 2014 , the Company recognized the following revenues attributable to the Janssen NV collaboration: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Royalty revenues (INCIVO) $ 59 $ 5,698 $ 1,584 $ 10,633 Collaborative revenues (telaprevir) 537 1,483 1,179 2,872 Total revenues attributable to the Janssen NV collaboration $ 596 $ 7,181 $ 2,763 $ 13,505
Fair Value Of Consideration Transferred	The consideration paid and the preliminary fair value of the contingent milestone and royalty payments payable by the Company pursuant to the agreement are set forth in the table below: June 4, 2015 (in thousands) Up-front payment $ 80,000 Fair value of contingent milestone and royalty payments 175,340 Total $ 255,340
Schedule of Recognized Identified Assets Acquired and Liabilities Assumed	The following table summarizes the preliminary fair values of the assets and liabilities recorded on the effective date of the agreement: June 4, 2015 (in thousands) Intangible assets $ 255,340 Goodwill 10,468 Deferred tax liability (91,023 ) Net other assets (liabilities) (10,468 ) Net assets attributable to noncontrolling interests $ 164,317
Schedule of Collaborative Arrangement Activity Net Loss Attributable to Noncontrolling Interest	The Company did not have any consolidated VIEs for the three and six months ended June 30, 2014. An aggregate summary of net loss attributable to noncontrolling interest related to the Company's VIEs for the three and six months ended June 30, 2015 is as follows: Three Months Ended June 30, 2015 Six Months Ended June 30, 2015 (in thousands) Loss attributable to noncontrolling interest before provision for income taxes $ (1,293 ) $ (1,579 ) Income tax provision (29,653 ) (29,590 ) Decrease in fair value of contingent milestone and royalty payments (1,198 ) (1,073 ) Net loss attributable to noncontrolling interest $ (32,144 ) $ (32,242 )
Schedule Of Collaborative Arrangement Summary Of Items Related To Variable Interest Entities	The following summarizes items related to the Company's VIEs included in the Company's condensed consolidated balance sheets as of the dates set forth in the table: June 30, 2015 December 31, 2014 (in thousands) Restricted cash and cash equivalents (VIE) $ 88,318 $ 8,418 Prepaid expenses and other current assets 895 268 Intangible assets 284,340 29,000 Goodwill 19,391 8,923 Other assets 508 42 Accounts payable 823 189 Accrued expenses and other current liabilities 34,254 3,891 Deferred tax liability, net 108,913 11,544 Other liabilities 6,068 300 Noncontrolling interest 153,252 21,177

Earnings Per Share (Tables)

Earnings Per Share (Tables)	6 Months Ended
	Jun. 30, 2015
Earnings Per Share [Abstract]
Potential gross common equivalent shares	The Company did not include the securities described in the following table in the computation of the net loss from continuing operations per share attributable to Vertex common shareholder calculations because the effect would have been anti-dilutive during each period: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Stock options 11,933 14,549 11,933 14,549 Unvested restricted stock and restricted stock units 3,355 2,584 3,355 2,584

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2015
Fair Value Disclosures [Abstract]
Financial assets subject to fair value measurements (excluding restricted cash and cash equivalents (Alios))	The following table sets forth the Company’s financial assets and liabilities subject to fair value measurements: Fair Value Measurements as of June 30, 2015 Fair Value Hierarchy Total Level 1 Level 2 Level 3 (in thousands) Financial assets carried at fair value: Cash equivalents: Money market funds $ 518,084 $ 518,084 $ — $ — Marketable securities: Corporate debt securities 120,408 — 120,408 — Commercial paper 25,499 — 25,499 — Prepaid and other current assets: Foreign currency forward contracts 1,087 — 1,087 — Total financial assets $ 665,078 $ 518,084 $ 146,994 $ — Financial liabilities carried at fair value: Other liabilities, current portion: Foreign currency forward contracts $ (2,737 ) $ — $ (2,737 ) $ — Other liabilities, excluding current portion: Foreign currency forward contracts (313 ) — (313 ) — Total financial liabilities $ (3,050 ) $ — $ (3,050 ) $ —

Marketable Securities (Tables)

Marketable Securities (Tables)	6 Months Ended
	Jun. 30, 2015
Cash and Cash Equivalents [Abstract]
Summary of cash, cash equivalents and marketable securities	A summary of the Company’s cash, cash equivalents and marketable securities is shown below: Amortized Cost Gross Gross Fair Value (in thousands) As of June 30, 2015 Cash and cash equivalents: Cash and money market funds $ 870,543 $ — $ — $ 870,543 Total cash and cash equivalents $ 870,543 $ — $ — $ 870,543 Marketable securities: Commercial paper (due within 1 year) $ 25,470 $ 29 $ — $ 25,499 Corporate debt securities (due within 1 year) 120,430 12 (34 ) 120,408 Total marketable securities $ 145,900 $ 41 $ (34 ) $ 145,907 Total cash, cash equivalents and marketable securities $ 1,016,443 $ 41 $ (34 ) $ 1,016,450 As of December 31, 2014 Cash and cash equivalents: Cash and money market funds $ 625,259 $ — $ — $ 625,259 Total cash and cash equivalents $ 625,259 $ — $ — $ 625,259 Marketable securities: Government-sponsored enterprise securities (due within 1 year) $ 463,788 $ 14 $ (52 ) $ 463,750 Commercial paper (due within 1 year) 51,674 72 — 51,746 Corporate debt securities (due within 1 year) 196,065 2 (66 ) 196,001 Corporate debt securities (due after 1 year through 5 years) 50,443 — (93 ) 50,350 Total marketable securities $ 761,970 $ 88 $ (211 ) $ 761,847 Total cash, cash equivalents and marketable securities $ 1,387,229 $ 88 $ (211 ) $ 1,387,106

Accumulated Other Comprehensi31

Accumulated Other Comprehensive Income (Loss) (Tables)	6 Months Ended
	Jun. 30, 2015
Equity [Abstract]
Accumulated Other Comprehensive Income (Loss)	A summary of the Company's changes in accumulated other comprehensive (loss) income by component is shown below: Foreign Currency Translation Adjustment Unrealized Holding Gains (Losses) on Marketable Securities Unrealized Gains (Losses) on Foreign Currency Forward Contracts Total (in thousands) Balance at December 31, 2014 $ (971 ) $ (123 ) $ 2,011 $ 917 Other comprehensive (loss) income before reclassifications 1,220 130 (1,370 ) (20 ) Amounts reclassified from accumulated other comprehensive loss — — (2,604 ) (2,604 ) Net current period other comprehensive (loss) income $ 1,220 $ 130 $ (3,974 ) $ (2,624 ) Balance at June 30, 2015 $ 249 $ 7 $ (1,963 ) $ (1,707 ) Foreign Currency Translation Adjustment Unrealized Holding Gains on Marketable Securities Unrealized Losses on Foreign Currency Forward Contracts Total (in thousands) Balance at December 31, 2013 $ (325 ) $ 42 $ (23 ) $ (306 ) Other comprehensive income (loss) before reclassifications 353 55 (108 ) 300 Amounts reclassified from accumulated other comprehensive loss — — (17 ) (17 ) Net current period other comprehensive income (loss) $ 353 $ 55 $ (125 ) $ 283 Balance at June 30, 2014 $ 28 $ 97 $ (148 ) $ (23 )

Hedging (Tables)

Hedging (Tables)	6 Months Ended
	Jun. 30, 2015
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Schedule of Cash Flow Hedging Instruments	The following table summarizes the notional amount of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges: As of June 30, 2015 As of December 31, 2014 Foreign Currency (in thousands) Euro $ 102,796 $ 20,209 British pound sterling 82,960 13,515 Australian dollar 25,993 — Total foreign currency forward contracts $ 211,749 $ 33,724
Schedule of Foreign Exchange Contracts	The following table summarizes the fair value of the Company's outstanding foreign currency forward contracts designated as cash flow hedges under GAAP included on the Company's condensed consolidated balance sheets: As of June 30, 2015 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 1,087 Other liabilities, current portion $ (2,737 ) Other assets — Other liabilities, excluding current portion (313 ) Total assets $ 1,087 Total liabilities $ (3,050 ) As of December 31, 2014 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 2,011 Other liabilities, current portion $ — Total assets $ 2,011 Total liabilities $ —
Derivatives Offsetting	The following table summarizes the potential effect of offsetting derivatives by type of financial instrument on the Company's condensed consolidated balance sheets: As of June 30, 2015 Gross Amounts Recognized Gross Amounts Offset Gross Amount Presented Gross Amount Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 1,087 $ — $ 1,087 $ (1,087 ) $ — Total liabilities $ (3,050 ) $ — $ (3,050 ) $ 1,087 $ (1,963 ) As of December 31, 2014 Gross Amounts Recognized Gross Amounts Offset Gross Amount Presented Gross Amount Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 2,011 $ — $ 2,011 $ — $ 2,011

Inventories (Tables)

Inventories (Tables)	6 Months Ended
	Jun. 30, 2015
Inventory Disclosure [Abstract]
Schedule of Inventories by Type	Inventories consisted of the following: As of June 30, 2015 As of December 31, 2014 (in thousands) Raw materials $ 8,147 $ 8,506 Work-in-process 30,989 20,508 Finished goods 2,977 1,834 Total $ 42,113 $ 30,848

Stock-based Compensation Expe34

Stock-based Compensation Expense (Tables)	6 Months Ended
	Jun. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-based compensation expense by line item	During the three and six months ended June 30, 2015 and 2014 , the Company recognized the following stock-based compensation expense included in loss from continuing operations: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Stock-based compensation expense by type of award: Stock options $ 37,687 $ 26,985 $ 66,646 $ 52,112 Restricted stock and restricted stock units 24,902 14,020 52,071 33,013 ESPP share issuances 1,825 1,681 3,965 4,348 Less stock-based compensation expense capitalized to inventories (1,153 ) (242 ) (2,037 ) (449 ) Total stock-based compensation included in costs and expenses $ 63,261 $ 42,444 $ 120,645 $ 89,024 Stock-based compensation expense by line item: Research and development expenses $ 41,632 $ 27,253 $ 79,849 $ 60,153 Sales, general and administrative expenses 21,629 15,191 40,796 28,871 Total stock-based compensation included in costs and expenses $ 63,261 $ 42,444 $ 120,645 $ 89,024
Unrecognized stock-based compensation expense, net of estimated forfeitures	The following table sets forth the Company's unrecognized stock-based compensation expense, net of estimated forfeitures, by type of award and the weighted-average period over which that expense is expected to be recognized: As of June 30, 2015 Unrecognized Expense, Weighted-average (in thousands) (in years) Type of award: Stock options $ 169,671 2.22 Restricted stock and restricted stock units $ 175,285 2.73 ESPP share issuances $ 3,953 0.59
Stock options outstanding and exercisable	The following table summarizes information about stock options outstanding and exercisable at June 30, 2015 : Options Outstanding Options Exercisable Range of Exercise Prices Number Weighted-average Weighted-average Number Weighted-average (in thousands) (in years) (per share) (in thousands) (per share) $17.16–$20.00 147 2.52 $ 18.87 147 $ 18.87 $20.01–$40.00 2,888 4.04 $ 34.82 2,534 $ 34.60 $40.01–$60.00 3,015 7.12 $ 48.32 1,534 $ 49.67 $60.01–$80.00 1,705 8.60 $ 75.99 539 $ 74.93 $80.01–$100.00 2,108 8.57 $ 90.22 621 $ 86.72 $100.01–$120.00 1,868 9.58 $ 109.24 113 $ 109.25 $120.01–$127.54 202 9.92 $ 127.31 165 $ 127.54 Total 11,933 7.22 $ 66.92 5,653 $ 52.06

Restructuring Liabilities (Tabl

Restructuring Liabilities (Tables)	6 Months Ended
	Jun. 30, 2015
Kendall Restructuring
Restructuring Cost and Reserve [Line Items]
Activity related to the restructuring liability	The activities related to the restructuring liability for the three and six months ended June 30, 2015 and 2014 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Liability, beginning of the period $ 9,506 $ 18,324 $ 11,596 $ 19,115 Cash payments (2,584 ) (3,960 ) (6,569 ) (7,822 ) Cash received from subleases 2,799 2,689 5,275 5,378 Restructuring expense (income) 203 (2,117 ) (378 ) (1,735 ) Liability, end of the period $ 9,924 $ 14,936 $ 9,924 $ 14,936
Fan Pier Move Restructuring
Restructuring Cost and Reserve [Line Items]
Activity related to the restructuring liability	The activities related to the restructuring liability for the three and six months ended June 30, 2015 and 2014 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Liability, beginning of the period $ 11,137 $ 3,722 $ 33,390 $ 797 Cash payments (3,095 ) (2,143 ) (22,351 ) (4,377 ) Restructuring expense (income) 975 1,677 (2,022 ) 6,836 Liability, end of the period $ 9,017 $ 3,256 $ 9,017 $ 3,256
Other Restructuring
Restructuring Cost and Reserve [Line Items]
Activity related to the restructuring liability	The activities related to the Company's other restructuring liabilities for the three and six months ended June 30, 2015 and 2014 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2015 2014 2015 2014 (in thousands) Liability, beginning of the period $ 845 $ 1,821 $ 869 $ 8,441 Cash payments (893 ) (1,199 ) (1,223 ) (8,466 ) Restructuring expense 950 170 1,256 817 Liability, end of the period $ 902 $ 792 $ 902 $ 792

Basis of Presentation and Acc36

Basis of Presentation and Accounting Policies (Details)	6 Months Ended
	Jun. 30, 2015segment
Accounting Policies [Abstract]
Number of operating segments	1

Product Revenues, Net (Details)

Product Revenues, Net (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2015USD ($)
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2014	$ 36,023
Provision related to current period sales	24,602
Adjustments related to prior period sales	(7,254)
Credits/payments made	(20,938)
Balance at June 30, 2015	32,433
Trade Allowances
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2014	1,463
Provision related to current period sales	2,865
Adjustments related to prior period sales	(86)
Credits/payments made	(2,985)
Balance at June 30, 2015	1,257
Rebates, Chargebacks and Discounts
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2014	29,102
Provision related to current period sales	20,305
Adjustments related to prior period sales	(5,958)
Credits/payments made	(13,654)
Balance at June 30, 2015	29,795
Product Returns
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2014	4,713
Provision related to current period sales	181
Adjustments related to prior period sales	(975)
Credits/payments made	(3,194)
Balance at June 30, 2015	725
Other Incentives
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2014	745
Provision related to current period sales	1,251
Adjustments related to prior period sales	(235)
Credits/payments made	(1,105)
Balance at June 30, 2015	$ 656

Collaborative Arrangements Co38

Collaborative Arrangements Collaborative Arrangements - Narrative (Details)	Jun. 04, 2015USD ($)	Oct. 31, 2014USD ($)	Apr. 30, 2011USD ($)	Jun. 30, 2015USD ($)	Dec. 31, 2014USD ($)	Jun. 30, 2014USD ($)	Mar. 31, 2013USD ($)	Sep. 30, 2012USD ($)	Jun. 30, 2015USD ($)payment	Jun. 30, 2014USD ($)	Dec. 31, 2014USD ($)
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative revenues				$ 611,000		$ 3,087,000			$ 1,453,000	$ 7,344,000
Development milestones discount rate low end of range (percentage)	4.10%
Development milestones discount rate high end of range (percentage)	5.90%
Commercial milestones and royalties discount rate (percentage)	6.60%
Intangible assets				284,340,000	$ 29,000,000				284,340,000		$ 29,000,000
BioAxone Biosciences Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Up-front payment					$ 10,000,000
License fees and milestone payments (up to)		$ 90,000,000
Collaborative Arrangements, Purchase Option, Term of Extension of Expiration Date		1 year
Increase (decrease) in fair value of contingent milestone and royalty payments				400,000					500,000
Business Combination, Contingent Consideration, Liability				27,600,000					27,600,000
Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Up-front payment	$ 80,000,000
Collaborative Arrangement, Prior to Marketing Approval, Time Period of Notice Required to Terminate	90 days
Collaborative Arrangement, Subsequent to Marketing Approval, Time Period of Notice Required to Terminate	180 days
Collaborative Arrangement, Change of Control Prior to Clinical Trial, Time Period of Notice Required to Terminate	30 days
Collaborative Arrangement, Term of Agreement Following First Commercial Sale	10 years
Business combination, consideration transferred	$ 255,340,000
Intangible assets	255,340,000
Increase (decrease) in fair value of contingent milestone and royalty payments				(1,600,000)
Business Combination, Contingent Consideration, Liability				173,700,000					173,700,000
Cystic Fibrosis Foundation Therapeutics Incorporated
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative funding			$ 75,000,000
Number of years over which funding will be made (in years)			5 years
Collaborative revenues				0		1,600,000			$ 0	4,500,000
Milestone payment made							$ 9,300,000	$ 9,300,000
Number of commercial milestone payments for achievement of certain sales levels for corrector compound such as VX-809 or VX-661 (in payments) | payment									2
Janssen
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative revenues				537,000		1,483,000			$ 1,179,000	2,872,000
Up-front payment											$ 35,000,000
Reimbursement revenue				$ 7,100,000		$ 0			$ 14,700,000	$ 0
Collaborative Arrangement, Time Period of Notice Required to Terminate									6 months
Additional Enac Inhibitors | Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum	230,000,000
Enac Inhibitors in Non Cf | Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum	370,000,000
ENaC Inhibitors in CF | Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum	490,000,000
Collaborative arrangement regulatory potential milestone payments maximum, global filling and approval	$ 360,000,000

Collaborative Arrangements Co39

Collaborative Arrangements Collaborative Arrangements (Details) - USD ($) $ in Thousands	Jun. 04, 2015	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014	Dec. 31, 2014
Recognized Collaborative Revenue [Abstract]
Royalty revenues		$ 5,077	$ 13,015	$ 11,869	$ 23,748
Collaborative revenues		611	3,087	1,453	7,344
Total revenues attributable to the Janssen NV collaboration		166,076	138,421	304,585	256,872
Business Combination, Recognized Identifiable Assets Acquired and Liabilities Assumed, Net [Abstract]
Intangible assets		284,340		284,340		$ 29,000
Goodwill		50,384		50,384		39,915
Deferred tax liability		(112,413)		(112,413)		(15,044)
Restricted cash and cash equivalents (VIE)		88,318		88,318		8,418
Prepaid expenses and other current assets		53,289		53,289		44,175
Other assets		9,136		9,136		3,265
Accounts payable		72,703		72,703		71,194
Accrued expenses		206,030		206,030		209,676
Other liabilities, excluding current portion		41,252		41,252		21,707
Noncontrolling interest		153,252		153,252		21,177
Loss attributable to noncontrolling interest before provision for income taxes		(190,861)	(158,396)	(389,266)	(389,704)
Income tax provision		(30,131)	(693)	(30,430)	(1,496)
Net loss attributable to noncontrolling interest		(32,144)	0	(32,242)	0
Janssen
Recognized Collaborative Revenue [Abstract]
Royalty revenues		59	5,698	1,584	10,633
Collaborative revenues		537	1,483	1,179	2,872
Total revenues attributable to the Janssen NV collaboration		596	$ 7,181	2,763	$ 13,505
Up-front payment						35,000
Parion Sciences, Inc
Recognized Collaborative Revenue [Abstract]
Up-front payment	$ 80,000
Fair value of contingent milestone and royalty payments	175,340
Business combination, consideration transferred	255,340
Business Combination, Recognized Identifiable Assets Acquired and Liabilities Assumed, Net [Abstract]
Intangible assets	255,340
Goodwill	10,468
Deferred tax liability	(91,023)
Net other assets (liabilities)	(10,468)
Net assets attributable to noncontrolling interests	$ 164,317
Income tax provision				(29,700)
Increase (decrease) in fair value of contingent milestone and royalty payments		(1,600)
Variable Interest Entity, Primary Beneficiary
Business Combination, Recognized Identifiable Assets Acquired and Liabilities Assumed, Net [Abstract]
Intangible assets		284,340		284,340		29,000
Goodwill		19,391		19,391		8,923
Deferred tax liability		(108,913)		(108,913)		(11,544)
Restricted cash and cash equivalents (VIE)		88,318		88,318		8,418
Prepaid expenses and other current assets		895		895		268
Other assets		508		508		42
Accounts payable		823		823		189
Accrued expenses		34,254		34,254		3,891
Other liabilities, excluding current portion		6,068		6,068		300
Noncontrolling interest		153,252		153,252		$ 21,177
Loss attributable to noncontrolling interest before provision for income taxes		(1,293)		(1,579)
Income tax provision		(29,653)		(29,590)
Increase (decrease) in fair value of contingent milestone and royalty payments		(1,198)		(1,073)
Net loss attributable to noncontrolling interest		$ (32,144)		$ (32,242)

Earnings Per Share (Details)

Earnings Per Share (Details) - shares shares in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	11,933	14,549	11,933	14,549
Unvested restricted stock and restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	3,355	2,584	3,355	2,584

Fair Value Measurements (Detail

Fair Value Measurements (Details) $ in Thousands	Jun. 30, 2015USD ($)
Level 3
Financial assets carried at fair value:
Term loan fair value	$ 294,800
Recurring basis
Financial assets carried at fair value:
Total financial assets	665,078
Total financial liabilities	(3,050)
Recurring basis | Money market funds
Financial assets carried at fair value:
Cash equivalents:	518,084
Recurring basis | Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	120,408
Recurring basis | Commercial paper
Financial assets carried at fair value:
Marketable securities:	25,499
Recurring basis | Level 1
Financial assets carried at fair value:
Total financial assets	518,084
Total financial liabilities	0
Recurring basis | Level 1 | Money market funds
Financial assets carried at fair value:
Cash equivalents:	518,084
Recurring basis | Level 1 | Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	0
Recurring basis | Level 1 | Commercial paper
Financial assets carried at fair value:
Marketable securities:	0
Recurring basis | Level 2
Financial assets carried at fair value:
Total financial assets	146,994
Total financial liabilities	(3,050)
Recurring basis | Level 2 | Money market funds
Financial assets carried at fair value:
Cash equivalents:	0
Recurring basis | Level 2 | Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	120,408
Recurring basis | Level 2 | Commercial paper
Financial assets carried at fair value:
Marketable securities:	25,499
Recurring basis | Level 3
Financial assets carried at fair value:
Total financial assets	0
Total financial liabilities	0
Recurring basis | Level 3 | Money market funds
Financial assets carried at fair value:
Cash equivalents:	0
Recurring basis | Level 3 | Corporate debt securities
Financial assets carried at fair value:
Marketable securities:	0
Recurring basis | Level 3 | Commercial paper
Financial assets carried at fair value:
Marketable securities:	0
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	1,087
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis | Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	1,087
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	(2,737)
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis | Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	(2,737)
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	(313)
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis | Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	(313)
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
Variable Interest Entity, Primary Beneficiary | BioAxone Biosciences Inc | Level 1
Financial assets carried at fair value:
Cash and cash equivalents	$ 84,400

Marketable Securities (Details)

Marketable Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Summary of cash, cash equivalents and marketable securities
Amortized Cost	$ 1,016,443	$ 1,387,229
Gross Unrealized Gains	41	88
Gross Unrealized Losses	(34)	(211)
Fair Value	1,016,450	1,387,106
Total cash and cash equivalents
Summary of cash, cash equivalents and marketable securities
Amortized Cost	870,543	625,259
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	870,543	625,259
Cash and money market funds
Summary of cash, cash equivalents and marketable securities
Amortized Cost	870,543	625,259
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	870,543	625,259
Total marketable securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	145,900	761,970
Gross Unrealized Gains	41	88
Gross Unrealized Losses	(34)	(211)
Fair Value	145,907	761,847
Government-sponsored enterprise securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost		463,788
Gross Unrealized Gains		14
Gross Unrealized Losses		(52)
Fair Value		463,750
Commercial paper (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	25,470	51,674
Gross Unrealized Gains	29	72
Gross Unrealized Losses	0	0
Fair Value	25,499	51,746
Corporate debt securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	120,430	196,065
Gross Unrealized Gains	12	2
Gross Unrealized Losses	(34)	(66)
Fair Value	$ 120,408	196,001
Corporate debt securities (due after 1 year through 5 years)
Summary of cash, cash equivalents and marketable securities
Amortized Cost		50,443
Gross Unrealized Gains		0
Gross Unrealized Losses		(93)
Fair Value		$ 50,350

Accumulated Other Comprehensi43

Accumulated Other Comprehensive Income (Loss) (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Accumulated Other Comprehensive Income (Loss), Net of Tax [Roll Forward]
Balance at balance sheet date			$ 917	$ (306)
Other comprehensive (loss) income before reclassifications			(20)	300
Amounts reclassified from accumulated other comprehensive loss			(2,604)	(17)
Total changes in other comprehensive loss	$ (2,498)	$ 274	(2,624)	283
Balance at balance sheet date	(1,707)	(23)	(1,707)	(23)
Foreign Currency Translation Adjustment
Accumulated Other Comprehensive Income (Loss), Net of Tax [Roll Forward]
Balance at balance sheet date			(971)	(325)
Other comprehensive (loss) income before reclassifications			1,220	353
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			1,220	353
Balance at balance sheet date	249	28	249	28
Unrealized Holding Gains (Losses) on Marketable Securities
Accumulated Other Comprehensive Income (Loss), Net of Tax [Roll Forward]
Balance at balance sheet date			(123)	42
Other comprehensive (loss) income before reclassifications			130	55
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			130	55
Balance at balance sheet date	7	97	7	97
Unrealized Gains (Losses) on Foreign Currency Forward Contracts
Accumulated Other Comprehensive Income (Loss), Net of Tax [Roll Forward]
Balance at balance sheet date			2,011	(23)
Other comprehensive (loss) income before reclassifications			(1,370)	(108)
Amounts reclassified from accumulated other comprehensive loss			(2,604)	(17)
Total changes in other comprehensive loss			(3,974)	(125)
Balance at balance sheet date	$ (1,963)	$ (148)	$ (1,963)	$ (148)

Hedging (Details)

Hedging (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets		$ 2,011
Fair Value - liabilities		0
Offsetting Derivative Assets [Abstract]
Gross Amounts Recognized	$ 1,087	2,011
Gross Amounts Offset	0	0
Gross Amount Presented	1,087	2,011
Gross Amount Not Offset	(1,087)	0
Legal Offset	0	2,011
Offsetting Derivative Liabilities [Abstract]
Gross Amounts Recognized	(3,050)
Gross Amounts Offset	0
Gross Amount Presented	(3,050)
Gross Amount Not Offset	1,087
Legal Offset	(1,963)
Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	211,749	33,724
Euro | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	102,796	20,209
British pound sterling | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	82,960	13,515
Australian dollar | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	25,993	0
Prepaid and other current assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	1,087	2,011
Other liabilities, current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(2,737)	$ 0
Other assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	0
Other liabilities, excluding current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	$ (313)

Inventories - Schedule of Inven

Inventories - Schedule of Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2015	Dec. 31, 2014
Inventory Disclosure [Abstract]
Raw materials	$ 8,147	$ 8,506
Work-in-process	30,989	20,508
Finished goods	2,977	1,834
Total	$ 42,113	$ 30,848

Intangible Assets and Goodwill

Intangible Assets and Goodwill (Details) - USD ($) $ in Thousands	1 Months Ended
	Oct. 31, 2014	Jun. 30, 2015	Jun. 04, 2015	Dec. 31, 2014
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets		$ 284,340		$ 29,000
Goodwill		50,384		39,915
Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets			$ 255,340
Goodwill			$ 10,468
Variable Interest Entity, Primary Beneficiary
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets		284,340		29,000
Goodwill		$ 19,391		$ 8,923
Variable Interest Entity, Primary Beneficiary | BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
In-process research and development intangible asset	$ 29,000
Indefinite-lived Intangible Assets | Variable Interest Entity, Primary Beneficiary | Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Fair value inputs, discount rate (percent)	7.10%
Indefinite-lived Intangible Assets | Variable Interest Entity, Primary Beneficiary | BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
Fair value inputs, discount rate (percent)	7.50%

Long-term Obligations - Fan Pie

Long-term Obligations - Fan Pier Leases (Details) $ in Thousands, ft² in Millions	12 Months Ended
	Dec. 31, 2011ft²leasebuilding	Jun. 30, 2015USD ($)	Dec. 31, 2014USD ($)
Property, Plant and Equipment [Line Items]
Number of leases | lease	2
Area of real estate property (in square feet) | ft²	1.1
Number of buildings under lease agreement | building	2
Optional term of lease agreement (in years)	10 years
Property, Plant and Equipment, Net		$ 713,378	$ 715,812
Construction financing lease obligation, current and noncurrent		473,200	473,400
Building
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Net		$ 508,900	$ 515,000

Long-term Obligations - Term Lo

Long-term Obligations - Term Loan (Details) - USD ($)	Jul. 09, 2014	Jun. 30, 2015
Senior Secured Term Loan
Debt Instrument [Line Items]
Face amount of term loan	$ 300,000,000
Interest rate, stated percentage	7.20%
Contingent interest rate (percent)	6.20%
Amount of principal repayment on quarterly installment payments through July 2016	$ 15,000,000
Amount of principal repayment on quarterly installment payments from October 2016	$ 60,000,000
Debt instrument, repayment provision, period over which present value of interest payments is determined	2 years
Unamortized discount on term loan	$ 5,300,000	$ 5,200,000
Senior Secured Term Loan Facility
Debt Instrument [Line Items]
Maximum borrowing capacity	$ 200,000,000
Minimum | Senior Secured Term Loan | LIBOR
Debt Instrument [Line Items]
Basis spread on variable rate (percent)	5.00%

Stock-based Compensation Expe49

Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Stock-based compensation expense:
Less stock-based compensation expense capitalized to inventories	$ (1,153)	$ (242)	$ (2,037)	$ (449)
Total stock-based compensation included in costs and expenses	63,261	42,444	120,645	89,024
Stock options
Stock-based compensation expense:
Stock-based compensation expense by type of award	37,687	26,985	66,646	52,112
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	169,671		$ 169,671
Weighted-average recognition period (in years)			2 years 2 months 19 days
Restricted stock and restricted stock units
Stock-based compensation expense:
Stock-based compensation expense by type of award	24,902	14,020	$ 52,071	33,013
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	175,285		$ 175,285
Weighted-average recognition period (in years)			2 years 8 months 23 days
ESPP share issuances
Stock-based compensation expense:
Stock-based compensation expense by type of award	1,825	1,681	$ 3,965	4,348
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	3,953		$ 3,953
Weighted-average recognition period (in years)			7 months 2 days
Research and development expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	41,632	27,253	$ 79,849	60,153
Sales, general and administrative expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	$ 21,629	$ 15,191	$ 40,796	$ 28,871
Stock and Option Plan 2013 [Member]
Type of award:
Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized	7,800,000

Stock-based Compensation Expe50

Stock-based Compensation Expense (Details 2) - Jun. 30, 2015 - $ / shares shares in Thousands	Total
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price range, options outstanding (in shares)	11,933
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 2 months 19 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 66.92
Exercise price range, options exercisable (in shares)	5,653
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 52.06
$17.16–$20.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	17.16
Exercise price, high end of range (usd per share)	$ 20
Exercise price range, options outstanding (in shares)	147
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	2 years 6 months 7 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 18.87
Exercise price range, options exercisable (in shares)	147
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 18.87
$20.01–$40.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	20.01
Exercise price, high end of range (usd per share)	$ 40
Exercise price range, options outstanding (in shares)	2,888
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	4 years 15 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 34.82
Exercise price range, options exercisable (in shares)	2,534
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 34.60
$40.01–$60.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	40.01
Exercise price, high end of range (usd per share)	$ 60
Exercise price range, options outstanding (in shares)	3,015
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 1 month 13 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 48.32
Exercise price range, options exercisable (in shares)	1,534
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 49.67
$60.01–$80.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	60.01
Exercise price, high end of range (usd per share)	$ 80
Exercise price range, options outstanding (in shares)	1,705
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 7 months 6 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 75.99
Exercise price range, options exercisable (in shares)	539
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 74.93
$80.01–$100.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	80.01
Exercise price, high end of range (usd per share)	$ 100
Exercise price range, options outstanding (in shares)	2,108
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 6 months 26 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 90.22
Exercise price range, options exercisable (in shares)	621
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 86.72
$100.01–$120.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	100.01
Exercise price, high end of range (usd per share)	$ 120
Exercise price range, options outstanding (in shares)	1,868
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 6 months 29 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 109.24
Exercise price range, options exercisable (in shares)	113
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 109.25
$120.01–$127.54
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	120.01
Exercise price, high end of range (usd per share)	$ 127.54
Exercise price range, options outstanding (in shares)	202
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 11 months 1 day
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 127.31
Exercise price range, options exercisable (in shares)	165
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 127.54

Other Arrangements (Details)

Other Arrangements (Details) - USD ($) $ in Millions	1 Months Ended	3 Months Ended	12 Months Ended
	Apr. 30, 2014	Jun. 30, 2014	Dec. 31, 2008	Jun. 30, 2015
Sale of HIV Protease Inhibitor Royalty Stream
Gross proceeds from sale of royalty rights receivable from GlaxoSmithKline			$ 160
Deferred revenue royalty purchase agreement				$ 35.4
Other Nonoperating Income	$ 36.7	$ 36.7

Income Taxes (Details)

Income Taxes (Details) - USD ($) $ in Thousands	Jun. 04, 2015	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014	Dec. 31, 2014
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes		$ 30,131	$ 693	$ 30,430	$ 1,496
Unrecognized tax benefits		900		900		$ 900
Estimated reduction in unrecognized tax benefits in next fiscal year		$ 500		500
Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes				$ 29,700
Up-front payment	$ 80,000

Restructuring Liabilities (Deta

Restructuring Liabilities (Details) ft² in Thousands	3 Months Ended		12 Months Ended
	Mar. 31, 2015ft²lease	Sep. 30, 2014facility	Dec. 31, 2003	Dec. 31, 2011ft²
Restructuring Cost and Reserve [Line Items]
Area of real estate property (in square feet)				1,100
Kendall Restructuring
Restructuring Cost and Reserve [Line Items]
Lease term (in years)			15 years
Restructuring and related activities, leased office space, maximum percentage used - not more than			50.00%
Fan Pier Move Restructuring
Restructuring Cost and Reserve [Line Items]
Number of facilities decommissioned | facility		3
Number of leases terminated | lease	2
Area of real estate property (in square feet)	120
Discount rate related to leases (percent)	9.00%

Restructuring Liabilities (De54

Restructuring Liabilities (Details 2) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2015	Jun. 30, 2014	Jun. 30, 2015	Jun. 30, 2014
Restructuring activities
Restructuring expense (income)	$ 2,128	$ (270)	$ (1,144)	$ 5,918
Kendall Restructuring
Restructuring activities
Liability, beginning of the period	9,506	18,324	11,596	19,115
Cash payments	(2,584)	(3,960)	(6,569)	(7,822)
Cash received from subleases	2,799	2,689	5,275	5,378
Restructuring expense (income)	203	(2,117)	(378)	(1,735)
Liability, end of the period	9,924	14,936	9,924	14,936
Fan Pier Move Restructuring
Restructuring activities
Liability, beginning of the period	11,137	3,722	33,390	797
Cash payments	(3,095)	(2,143)	(22,351)	(4,377)
Restructuring expense (income)	975	1,677	(2,022)	6,836
Liability, end of the period	9,017	3,256	9,017	3,256
Other Restructuring
Restructuring activities
Liability, beginning of the period	845	1,821	869	8,441
Cash payments	(893)	(1,199)	(1,223)	(8,466)
Restructuring expense (income)	950	170	1,256	817
Liability, end of the period	$ 902	$ 792	$ 902	$ 792

Commitments and Contingencies (

Commitments and Contingencies (Details) $ in Millions	Jun. 30, 2015USD ($)
Commitments and Contingencies Disclosure [Abstract]
Restricted cash and cash equivalents	$ 21.9