Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Sep. 30, 2013		Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 583,181	[1]	$ 489,407	[1]
Marketable securities, available for sale	839,469	[1]	831,808	[1]
Restricted cash and cash equivalents (Alios)	51,059	[1]	69,983	[1]
Accounts receivable, net	120,281	[1]	143,250	[1]
Inventories	13,537	[1]	30,464	[1]
Prepaid expenses and other current assets	41,104	[1]	24,673	[1]
Total current assets	1,648,631	[1]	1,589,585	[1]
Restricted cash	127	[1]	31,934	[1]
Property and equipment, net	648,924	[1]	433,609	[1]
Intangible assets	250,600	[1]	663,500	[1]
Goodwill	30,992	[1]	30,992	[1]
Other assets	3,474	[1]	9,668	[1]
Total assets	2,582,748	[1]	2,759,288	[1]
Current liabilities:
Accounts payable	51,533	[1]	101,292	[1]
Accrued expenses	280,848	[1]	264,884	[1]
Deferred revenues, current portion	31,007	[1]	27,566	[1]
Accrued restructuring expense, current portion	9,858	[1]	4,758	[1]
Capital lease obligations, current portion	14,429	[1]	13,707	[1]
Other liabilities, current portion	21,824	[1]	20,417	[1]
Total current liabilities	409,499	[1]	432,624	[1]
Deferred revenues, excluding current portion	77,354	[1]	96,242	[1]
Accrued restructuring expense, excluding current portion	16,280	[1]	18,570	[1]
Capital lease obligations, excluding current portion	39,381	[1]	15,170	[1]
Convertible senior subordinated notes (due 2015)	0	[1]	400,000	[1]
Deferred tax liability	150,203	[1]	280,367	[1]
Construction financing lease obligation	392,569	[1]	268,031	[1]
Other liabilities, excluding current portion	10,782	[1]	13,902	[1]
Total liabilities	1,096,068	[1]	1,524,906	[1]
Commitments and contingencies		[1]		[1]
Redeemable noncontrolling interest (Alios)	39,624	[1]	38,530	[1]
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at September 30, 2013 and December 31, 2012	0	[1]	0	[1]
Common stock, $0.01 par value; 300,000,000 shares authorized at September 30, 2013 and December 31, 2012; 233,592,201 and 217,286,868 shares issued and outstanding at September 30, 2013 and December 31, 2012, respectively	2,311	[1]	2,149	[1]
Additional paid-in capital	5,274,307	[1]	4,519,448	[1]
Accumulated other comprehensive loss	(550)	[1]	(550)	[1]
Accumulated deficit	(4,011,180)	[1]	(3,521,867)	[1]
Total Vertex shareholders’ equity	1,264,888	[1]	999,180	[1]
Noncontrolling interest (Alios)	182,168	[1]	196,672	[1]
Total shareholders’ equity	1,447,056	[1]	1,195,852	[1]
Total liabilities and shareholders’ equity	$ 2,582,748	[1]	$ 2,759,288	[1]

[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.