Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Jun. 30, 2013		Dec. 31, 2012
Current assets:
Cash and cash equivalents	$ 531,247	[1]	$ 489,407	[1]
Marketable securities, available for sale	899,449	[1]	831,808	[1]
Restricted cash and cash equivalents (Alios)	58,288	[1]	69,983	[1]
Accounts receivable, net	164,866	[1]	143,250	[1]
Inventories	19,509	[1]	30,464	[1]
Prepaid expenses and other current assets	43,231	[1]	24,673	[1]
Total current assets	1,716,590	[1]	1,589,585	[1]
Restricted cash	122	[1]	31,934	[1]
Property and equipment, net	581,738	[1]	433,609	[1]
Intangible assets	250,600	[1]	663,500	[1]
Goodwill	30,992	[1]	30,992	[1]
Other assets	4,287	[1]	9,668	[1]
Total assets	2,584,329	[1]	2,759,288	[1]
Current liabilities:
Accounts payable	48,570	[1]	101,292	[1]
Accrued expenses	260,849	[1]	264,884	[1]
Deferred revenues, current portion	32,900	[1]	27,566	[1]
Accrued restructuring expense, current portion	5,047	[1]	4,758	[1]
Capital lease obligations, current portion	10,664	[1]	13,707	[1]
Other liabilities, current portion	23,622	[1]	20,417	[1]
Total current liabilities	381,652	[1]	432,624	[1]
Deferred revenues, excluding current portion	84,066	[1]	96,242	[1]
Accrued restructuring expense, excluding current portion	17,005	[1]	18,570	[1]
Capital lease obligations, excluding current portion	28,088	[1]	15,170	[1]
Convertible senior subordinated notes (due 2015)	0	[1]	400,000	[1]
Deferred tax liability	149,706	[1]	280,367	[1]
Construction financing lease obligation	359,100	[1]	268,031	[1]
Other liabilities, excluding current portion	16,049	[1]	13,902	[1]
Total liabilities	1,035,666	[1]	1,524,906	[1]
Commitments and contingencies		[1]		[1]
Redeemable noncontrolling interest (Alios)	39,214	[1]	38,530	[1]
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at June 30, 2013 and December 31, 2012	0	[1]	0	[1]
Common stock, $0.01 par value; 300,000,000 shares authorized at June 30, 2013 and December 31, 2012; 232,176,564 and 217,286,868 shares issued and outstanding at June 30, 2013 and December 31, 2012, respectively	2,300	[1]	2,149	[1]
Additional paid-in capital	5,208,431	[1]	4,519,448	[1]
Accumulated other comprehensive loss	(1,230)	[1]	(550)	[1]
Accumulated deficit	(3,887,048)	[1]	(3,521,867)	[1]
Total Vertex shareholders’ equity	1,322,453	[1]	999,180	[1]
Noncontrolling interest (Alios)	186,996	[1]	196,672	[1]
Total shareholders’ equity	1,509,449	[1]	1,195,852	[1]
Total liabilities and shareholders’ equity	$ 2,584,329	[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.