CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (USD $) In Thousands, unless otherwise specified	Total	Common stock	Additional paid in capital	Accumulated other comprehensive income	Accumulated deficit	Regulus	Ibis	Comprehensive income (loss)
Balance at Dec. 31, 2008	$ 147,380	$ 97	$ 960,361	$ 982	$ (851,216)	$ 4,737	$ 32,419
Balance (in shares) at Dec. 31, 2008		97,172
Comprehensive income (loss):
Net income (loss)	150,672				155,066	(4,394)		150,672
Change in unrealized gains (losses), net of $0.8 million of tax expense in 2009	2,819			2,819				2,819
Reclassification adjustment for realized gains (losses) included in net income (loss)	(1,648)			(1,648)				(1,648)
Comprehensive income (loss)	151,843							151,843
Options exercised and employee stock purchase plan issuances	13,156	2	13,154
Options exercised and employee stock purchase plan issuances (in shares)		1,670
Warrants exercised (in shares)		9
Excess tax benefits on share-based compensation	278		278
Share-based compensation expense	11,827		11,827
Sale of Ibis to AMI	(32,419)						(32,419)
Alnylam's capital contribution to noncontrolling interest	10,000					10,000
Balance at Dec. 31, 2009	302,065	99	985,620	2,153	(696,150)	10,343
Balance (in shares) at Dec. 31, 2009		98,851
Increase (Decrease) in Stockholders' Equity
Regulus Therapeutics Inc. (Adoption of accounting standard to deconsolidate)	(11,583)		(1,954)		714	(10,343)
Comprehensive income (loss):
Net income (loss)	(61,251)				(61,251)			(61,251)
Change in unrealized gains (losses), net of $0.8 million of tax expense in 2009	(1,342)			(1,342)				(1,342)
Reclassification adjustment for realized gains (losses) included in net income (loss)	138			138				138
Comprehensive income (loss)	(62,455)							(62,455)
Options exercised and employee stock purchase plan issuances	4,356		4,356
Options exercised and employee stock purchase plan issuances (in shares)		475
Warrants exercised (in shares)		68
Share-based compensation expense	12,159		12,159
Balance at Dec. 31, 2010	244,542	99	1,000,181	949	(756,687)
Balance (in shares) at Dec. 31, 2010		99,394
Comprehensive income (loss):
Net income (loss)	(84,801)				(84,801)			(84,801)
Change in unrealized gains (losses), net of $0.8 million of tax expense in 2009	(1,719)			(1,719)				(1,719)
Comprehensive income (loss)	(86,520)							(86,520)
Options exercised and employee stock purchase plan issuances	3,567	1	3,566
Options exercised and employee stock purchase plan issuances (in shares)		646
Warrants exercised (in shares)		3
Share-based compensation expense	9,845		9,845
Balance at Dec. 31, 2011	$ 171,434	$ 100	$ 1,013,592	$ (770)	$ (841,488)
Balance (in shares) at Dec. 31, 2011		100,043