Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012		Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 436,886		$ 475,320
Marketable securities, available for sale	861,656		493,602
Restricted cash and cash equivalents (Alios)	74,954	[1]	51,878	[1]
Accounts receivable, net	139,629		183,135
Inventories	86,275		112,430
Prepaid expenses and other current assets	35,123	[1]	14,889	[1]
Total current assets	1,634,523		1,331,254
Restricted cash	32,166		34,090
Property and equipment, net	124,148	[1]	78,106	[1]
Fan Pier buildings	223,101		55,070
Intangible assets	663,500	[1]	663,500	[1]
Goodwill	30,992	[1]	30,992	[1]
Other assets	10,393	[1]	11,268	[1]
Total assets	2,718,823		2,204,280
Current liabilities:
Accounts payable	83,732	[1]	74,642	[1]
Accrued expenses	273,285	[1]	255,662	[1]
Deferred revenues, current portion	27,303		45,037
Accrued restructuring expense, current portion	4,596		4,932
Other liabilities, current portion	13,944
Income taxes payable (Alios)	3,871	[1]	12,075	[1]
Total current liabilities	406,731		392,348
Deferred revenues, excluding current portion	103,626		118,095
Accrued restructuring expense, excluding current portion	19,559		21,381
Convertible senior subordinated notes (due 2015)	400,000		400,000
Deferred tax liability	279,466	[1]	243,707	[1]
Construction financing obligation	215,956		55,950
Other liabilities, excluding current portion	28,739	[1]	7,287	[1]
Total liabilities	1,454,077		1,238,768
Commitments and contingencies:
Redeemable noncontrolling interest (Alios)	38,299	[1]	37,036	[1]
Shareholders' equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at September 30, 2012 and December 31, 2011
Common stock, $0.01 par value; 300,000,000 shares authorized; 216,341,505 and 209,303,995 shares issued and outstanding at September 30, 2012 and December 31, 2011, respectively	2,141		2,072
Additional paid-in capital	4,471,727		4,200,659
Accumulated other comprehensive loss	(416)		(1,053)
Accumulated deficit	(3,445,719)		(3,414,835)
Total Vertex shareholders' equity	1,027,733		786,843
Noncontrolling interest (Alios)	198,714	[1]	141,633	[1]
Total shareholders' equity	1,226,447		928,476
Total liabilities and shareholders' equity	$ 2,718,823		$ 2,204,280

[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.