Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Mar. 31, 2013		Mar. 31, 2012
Cash flows from operating activities:
Net income (loss)	$ (312,627)		$ 87,876
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization expense	10,691		8,560
Stock-based compensation expense	31,275		27,688
Other non-cash based compensation expense	2,432		2,292
Intangible asset impairment charge	412,900		0
Deferred income taxes	(128,703)		(2,281)
Loss on disposal of property and equipment	23		0
Other non-cash items, net	(998)		18
Changes in operating assets and liabilities:
Accounts receivable, net	(48,834)		(49,093)
Inventories	9,231		(16,915)
Prepaid expenses and other current assets	(24,986)		(20,541)
Accounts payable	(40,571)		(1,400)
Accrued expenses and other liabilities	23,236		(15,769)
Excess tax benefit from share-based payment arrangements	0		(227)
Accrued restructuring expense	(869)		(840)
Deferred revenues	2,022		(16,452)
Net cash provided by (used in) operating activities	(65,778)		2,916
Cash flows from investing activities:
Purchases of marketable securities	(458,971)		(403,179)
Sales and maturities of marketable securities	430,535		183,987
Expenditures for property and equipment	(16,607)		(6,155)
Decrease (increase) in restricted cash and cash equivalents (Alios)	6,975		(6,139)
Decrease (increase) in other assets	472		(216)
Net cash used in investing activities	(37,596)		(231,702)
Cash flows from financing activities:
Excess tax benefit from share-based payment arrangements	0		227
Issuances of common stock from employee benefit plans	21,670		21,298
Payments on capital lease obligations	(10,096)		0
Payments on construction financing lease obligation	(17,709)		0
Net cash provided by (used in) financing activities	(6,135)		21,525
Effect of changes in exchange rates on cash	(799)		(136)
Net increase (decrease) in cash and cash equivalents	(110,308)		(207,397)
Cash and cash equivalents—beginning of period	489,407	[1]	475,320
Cash and cash equivalents—end of period	379,099	[1]	267,923
Supplemental disclosure of cash flow information:
Cash paid for income taxes	1,541		0
Capitalization of construction in-process related to construction financing lease obligation	$ 66,052		$ 38,229

[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.