Collaborative Arrangements and Licensing Agreements (Details) (USD $) Share data in Millions, unless otherwise specified	3 Months Ended				12 Months Ended	1 Months Ended	3 Months Ended	0 Months Ended			1 Months Ended	3 Months Ended			1 Months Ended	3 Months Ended			1 Months Ended			3 Months Ended			3 Months Ended					1 Months Ended		3 Months Ended			1 Months Ended		3 Months Ended							1 Months Ended								3 Months Ended			1 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013 Collaborations Biogen Idec	Mar. 31, 2012 Collaborations Biogen Idec	Dec. 31, 2012 Collaborations Biogen Idec item	Jan. 31, 2012 Collaborations Biogen Idec Agreement entered into in January 2012	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Phase 2/3 item	May 31, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Phase 2/3 Forecast	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Development milestones	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Regulatory milestones	Jun. 30, 2012 Collaborations Biogen Idec Agreement entered into in June 2012	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in June 2012 IND-enabling toxicology study	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in June 2012 Development milestones	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in June 2012 Regulatory milestones	Dec. 31, 2012 Collaborations Biogen Idec Agreement entered into in December 2012 item	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in December 2012 IND-enabling toxicology study	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in December 2012 Clinical and regulatory milestones	Mar. 31, 2013 Collaborations Biogen Idec Agreement entered into in December 2012 Regulatory milestones	Jan. 31, 2013 Collaborations Genzyme Corporation	May 31, 2012 Collaborations Genzyme Corporation	Jan. 31, 2008 Collaborations Genzyme Corporation	Mar. 31, 2013 Collaborations Genzyme Corporation	Mar. 31, 2012 Collaborations Genzyme Corporation	Dec. 31, 2012 Collaborations Genzyme Corporation	Mar. 31, 2013 Collaborations Genzyme Corporation Minimum	Mar. 31, 2013 Collaborations Genzyme Corporation Maximum	Mar. 31, 2013 Collaborations Genzyme Corporation Pre-specified events	Mar. 31, 2013 Collaborations Genzyme Corporation Regulatory milestones	Mar. 31, 2013 Collaborations Genzyme Corporation Commercialization milestones	Feb. 28, 2013 Collaborations Glaxo Smith Kline	Oct. 31, 2012 Collaborations Glaxo Smith Kline item	Mar. 31, 2013 Collaborations Glaxo Smith Kline item	Mar. 31, 2012 Collaborations Glaxo Smith Kline	Dec. 31, 2012 Collaborations Glaxo Smith Kline	Dec. 31, 2012 Collaborations Glaxo Smith Kline ISIS-TTR	Mar. 31, 2013 Collaborations Glaxo Smith Kline Up to Phase 2 proof-of-concept	Mar. 31, 2013 Collaborations Glaxo Smith Kline Phase 2/3 ISIS-TTR	Mar. 31, 2013 Collaborations Glaxo Smith Kline Pre-specified events	Mar. 31, 2013 Collaborations Glaxo Smith Kline Development milestones	Mar. 31, 2013 Collaborations Glaxo Smith Kline Development milestones ISIS-TTR	Mar. 31, 2013 Collaborations Glaxo Smith Kline Pre-licensing milestones Phase 2/3 ISIS-TTR	Mar. 31, 2013 Collaborations Glaxo Smith Kline Regulatory milestones	Mar. 31, 2013 Collaborations Glaxo Smith Kline Commercialization milestones	Apr. 30, 2013 Collaborations Roche Subsequent Event	Apr. 30, 2013 Collaborations Roche Drug targeting HTT protein Subsequent Event	Apr. 30, 2013 Collaborations Roche Pre-specified events Drug targeting HTT protein Subsequent Event	Apr. 30, 2013 Collaborations Roche Pre-specified events Additional drugs Subsequent Event	Apr. 30, 2013 Collaborations Roche Development milestones Drug targeting HTT protein Subsequent Event	Apr. 30, 2013 Collaborations Roche Regulatory milestones Drug targeting HTT protein Subsequent Event	Apr. 30, 2013 Collaborations Roche Commercialization milestones Drug targeting HTT protein Subsequent Event	Apr. 30, 2013 Collaborations Roche Commercialization milestones Drug using Roche's proprietary brain shuttle technology Subsequent Event	Mar. 31, 2013 Collaborations CHDI Foundation, Inc.	Mar. 31, 2012 Collaborations CHDI Foundation, Inc.	Dec. 31, 2012 Collaborations CHDI Foundation, Inc.	Apr. 30, 2013 Collaborations CHDI Foundation, Inc. Subsequent Event	Apr. 30, 2013 Collaborations CHDI Foundation, Inc. Development milestones Forecast Subsequent Event
Collaborations
Number of targets															3
Upfront fee received						$ 29,000,000					$ 12,000,000				$ 30,000,000																				$ 2,500,000									$ 30,000,000
Number of collaborations					3
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%
Maximum number of programs under strategic alliance																																6
Number of programs under strategic alliance, not accelerated																															5
Milestone payment recognized								3,500,000											25,000,000			25,000,000								7,500,000		7,500,000
Cumulative payments earned under collaborative arrangement at period end																																								17,500,000
Maximum amount of payments receivable									45,000,000	150,000,000			59,000,000	130,000,000													1,500,000,000	700,000,000	825,000,000									1,300,000,000	231,500,000		50,000,000	594,500,000	545,000,000			362,000,000		67,000,000	170,000,000	80,000,000	50,000,000
Number of milestones payments							4
Next prospective milestone							18,000,000					10,000,000				10,000,000						25,000,000															2,000,000								22,000,000
Maximum amount of payments receivable per drug under strategic alliance																10,000,000	200,000,000	130,000,000																													136,500,000
Minimum annual net revenues to earn next milestone payment																						250,000,000
Initial development cost contributed																						125,000,000
Period following an acquisition within which collaborator may purchase rights to receive payments																						180 days
Period for which additional shares of Isis common stock will not be purchased without consent																					10 years
Ownership percentage of Isis stock below which strategic partner may acquire additional shares without prior consent																						2.00%
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
Revenue earned	43,360,000	23,235,000	3,900,000	1,800,000																		25,000,000	16,400,000									9,900,000	2,000,000																			293,000	1,200,000
Percent of total revenue																						58.00%	71.00%									23.00%	9.00%
Deferred revenue			59,200,000		62,600,000																	3,800,000		3,800,000								17,600,000		19,900,000																				229,000
Average maximum milestone payments receivable per program																																				20,000,000
Expense reimbursement paid																																																							$ 1,500,000	$ 1,500,000