Collaborative Arrangements and Licensing Agreements (Details) (USD $) Share data in Millions, unless otherwise specified	3 Months Ended		9 Months Ended		3 Months Ended	9 Months Ended	1 Months Ended	9 Months Ended			1 Months Ended		9 Months Ended			1 Months Ended		3 Months Ended			9 Months Ended			9 Months Ended					3 Months Ended	9 Months Ended						1 Months Ended	3 Months Ended		9 Months Ended			1 Months Ended	9 Months Ended		1 Months Ended					1 Months Ended		3 Months Ended	9 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012	Sep. 30, 2011	Sep. 30, 2012 Collaborations Biogen Idec	Sep. 30, 2012 Collaborations Biogen Idec	Jan. 31, 2012 Collaborations Biogen Idec Agreement entered into in January 2012	Sep. 30, 2012 Collaborations Biogen Idec Agreement entered into in January 2012 Phase 2/3	Sep. 30, 2012 Collaborations Biogen Idec Agreement entered into in January 2012 Development milestones	Sep. 30, 2012 Collaborations Biogen Idec Agreement entered into in January 2012 Pre-specified regulatory milestones	Jul. 31, 2012 Collaborations Biogen Idec Agreement entered into in June 2012	Jun. 30, 2012 Collaborations Biogen Idec Agreement entered into in June 2012	Sep. 30, 2012 Collaborations Biogen Idec Agreement entered into in June 2012 IND-enabling toxicology study	Sep. 30, 2012 Collaborations Biogen Idec Agreement entered into in June 2012 Development milestones	Sep. 30, 2012 Collaborations Biogen Idec Agreement entered into in June 2012 Pre-specified regulatory milestones	May 31, 2012 Collaborations Genzyme Corporation	Jun. 30, 2008 Collaborations Genzyme Corporation	Sep. 30, 2012 Collaborations Genzyme Corporation	Jun. 30, 2012 Collaborations Genzyme Corporation	Sep. 30, 2011 Collaborations Genzyme Corporation	Sep. 30, 2012 Collaborations Genzyme Corporation	Sep. 30, 2011 Collaborations Genzyme Corporation	Dec. 31, 2011 Collaborations Genzyme Corporation	Sep. 30, 2012 Collaborations Genzyme Corporation Minimum	Sep. 30, 2012 Collaborations Genzyme Corporation Maximum	Sep. 30, 2012 Collaborations Genzyme Corporation Commercialization milestones	Sep. 30, 2012 Collaborations Genzyme Corporation Regulatory milestones	Sep. 30, 2012 Collaborations Genzyme Corporation Pre-specified events	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc.	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc.	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc. Phase 2	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc. Development milestones	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc. Commercialization milestones	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc. Regulatory milestones	Sep. 30, 2012 Collaborations Xenon Pharmaceuticals Inc. Pre-specified events	Mar. 31, 2010 Collaborations Glaxo Smith Kline item	Sep. 30, 2012 Collaborations Glaxo Smith Kline	Sep. 30, 2011 Collaborations Glaxo Smith Kline	Sep. 30, 2012 Collaborations Glaxo Smith Kline	Sep. 30, 2011 Collaborations Glaxo Smith Kline	Dec. 31, 2011 Collaborations Glaxo Smith Kline	Oct. 31, 2012 Collaborations Glaxo Smith Kline Forecast	Sep. 30, 2012 Collaborations Glaxo Smith Kline Phase 2/3	Sep. 30, 2012 Collaborations Glaxo Smith Kline Phase 2	Oct. 31, 2012 Collaborations Glaxo Smith Kline Development milestones	Sep. 30, 2012 Collaborations Glaxo Smith Kline Development milestones	Oct. 31, 2012 Collaborations Glaxo Smith Kline Pre-licensing milestones Phase 2/3	Sep. 30, 2012 Collaborations Glaxo Smith Kline Commercialization milestones	Sep. 30, 2012 Collaborations Glaxo Smith Kline Regulatory milestones	Oct. 31, 2012 Collaborations Alnylam	Mar. 31, 2004 Collaborations Alnylam	Sep. 30, 2012 Collaborations Alnylam	Sep. 30, 2012 Collaborations Alnylam	Sep. 30, 2012 Collaborations Alnylam Development milestones	Sep. 30, 2012 Collaborations Alnylam Regulatory milestones	Sep. 30, 2012 Collaborations Alnylam Pre-specified events	Sep. 30, 2012 Collaborations Alnylam Development and regulatory milestones
Collaborations
Maximum value of collaboration agreement							$ 299,000,000					$ 271,000,000
Upfront fee received							29,000,000				12,000,000																												35,000,000			2,500,000
Maximum amount of payments receivable									45,000,000	150,000,000				59,000,000	130,000,000
Next prospective milestone								18,000,000					10,000,000								25,000,000										3,000,000												7,500,000
Deferred revenue					35,000,000	35,000,000												5,600,000			5,600,000		27,700,000														19,400,000		19,400,000		25,300,000
Revenue earned					2,400,000	6,000,000												4,700,000		16,600,000	63,900,000	49,900,000							84,000	84,000							2,100,000	2,000,000	6,000,000	10,700,000										1,100,000		1,600,000	1,600,000
License fee received																	175,000,000
Equity investment in entity made by strategic alliance partner																	150,000,000
Equity investment in entity made by strategic alliance partner (in shares)																	5
Profit share as percentage of commercial sales																								30.00%	50.00%
Milestone payment received																25,000,000																													10,000,000
Initial development cost contributed																					125,000,000
Period following an acquisition within which collaborator may purchase rights to receive payments																					180 days
Isis stock ownership percentage must be less than this percentage for strategic partner to acquire additional Isis common stock without prior consent																		2.00%			2.00%
Maximum period additional shares of Isis common stock will not be purchased without consent																	10 years
Premium for which amortization was completed during the period																100,000,000
License fee for which amortization was completed during the period																175,000,000
Percent of total revenue					21.00%	7.00%												41.00%			78.00%																18.00%		7.00%													13.00%	2.00%
Maximum amount of milestone payments receivable under strategic alliance																										825,000,000	725,000,000	1,500,000,000				26,000,000	120,000,000	150,000,000	296,000,000		1,300,000,000		1,300,000,000							239,000,000	50,000,000	545,000,000	594,500,000					1,100,000	2,300,000	3,400,000
Technology access fee																																																			5,000,000
Maximum amount of milestone payments payable under strategic alliance																																																									3,400,000
Research and development revenue under collaborative agreements	11,127,000	20,189,000	80,085,000	64,508,000
Cumulative sublicensing revenue recognized under collaborative arrangement																																																		39,800,000
Maximum number of programs under strategic alliance																																				6
Cumulative revenue recognized under collaborative arrangement at period end																																					53,000,000		53,000,000
Milestone payment recognized																			25,000,000																				15,000,000
Amount received from expansion of collaboration																																							3,000,000
Average maximum milestone payments receivable																																												$ 20,000,000