Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2013		Sep. 30, 2012
Cash flows from operating activities:
Net income (loss)	$ (503,001)		$ 26,941
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization expense	30,734		25,818
Stock-based compensation expense	103,933		86,649
Other non-cash based compensation expense	5,856		8,070
Intangible asset impairment charge	412,900		0
Deferred income taxes	(130,164)		35,759
Asset impairment charges	6,650		0
Write-down of inventories to net realizable value	10,358		78,000
Other non-cash items, net	(1,393)		(304)
Changes in operating assets and liabilities:
Accounts receivable, net	20,737		43,538
Inventories	(5,212)		32,419
Prepaid expenses and other current assets	(16,477)		(22,698)
Accounts payable	(46,005)		1,359
Accrued expenses and other liabilities	32,872		12,027
Excess tax benefit from share-based payment arrangements	0		1,097
Accrued restructuring expense	2,810		(2,158)
Deferred revenues	(15,447)		(32,203)
Net cash provided by (used in) operating activities	(80,425)		227,282
Cash flows from investing activities:
Purchases of marketable securities	(1,850,015)		(1,309,044)
Sales and maturities of marketable securities	1,842,361		941,314
Expenditures for property and equipment	(36,922)		(43,094)
Decrease in restricted cash and cash equivalents	31,807		1,923
Decrease (increase) in restricted cash and cash equivalents (Alios)	18,924		(23,075)
Decrease (increase) in other assets	(1,094)		997
Net cash provided by (used in) investing activities	7,249		(432,973)
Cash flows from financing activities:
Excess tax benefit from share-based payment arrangements	0		1,097
Issuances of common stock from employee benefit plans	242,360		174,950
Payments to redeem secured notes (due 2015)	(158)		0
Payments on capital lease obligations	(14,601)		(2,408)
Payments on construction financing lease obligation	(63,242)		(6,272)
Net cash provided by (used in) financing activities	164,359		167,367
Effect of changes in exchange rates on cash	2,591		(110)
Net increase (decrease) in cash and cash equivalents	93,774		(38,434)
Cash and cash equivalents—beginning of period	489,407	[1]	475,320
Cash and cash equivalents—end of period	583,181	[1]	436,886
Supplemental disclosure of cash flow information:
Cash paid for interest	6,700		6,700
Conversion of convertible senior subordinated notes (due 2015) for common stock	399,842		0
Interest on converted convertible senior subordinated notes (due 2015) offset to additional paid-in capital	6,700		0
Unamortized debt issuance costs of converted convertible subordinated notes (due 2015) offset to additional paid-in capital	4,230		0
Capitalization of construction in-process related to construction financing lease obligation	176,484		167,996
Assets acquired under capital lease	$ 38,520		$ 27,552

[1] Amounts include the assets and liabilities of Vertex’s variable interest entity (“VIE”), Alios BioPharma, Inc. (“Alios”). Vertex’s interests and obligations with respect to the VIE’s assets and liabilities are limited to those accorded to Vertex in its agreement with Alios. See Note C, "Collaborative Arrangements," to these condensed consolidated financial statements for amounts.