Collaborative Arrangements and Licensing Agreements (Details) (USD $)	1 Months Ended	3 Months Ended		6 Months Ended		1 Months Ended		3 Months Ended	6 Months Ended	7 Months Ended	6 Months Ended		6 Months Ended			3 Months Ended		6 Months Ended		12 Months Ended	1 Months Ended	6 Months Ended			1 Months Ended	6 Months Ended			1 Months Ended	6 Months Ended			1 Months Ended			3 Months Ended			6 Months Ended			6 Months Ended					1 Months Ended	3 Months Ended		6 Months Ended			1 Months Ended		6 Months Ended			1 Months Ended					1 Months Ended	3 Months Ended	6 Months Ended								3 Months Ended	6 Months Ended	1 Months Ended	3 Months Ended	6 Months Ended					1 Months Ended	3 Months Ended	6 Months Ended
	Jun. 30, 2013	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013 Collaborations AstraZeneca	Dec. 31, 2012 Collaborations AstraZeneca item	Jun. 30, 2013 Collaborations AstraZeneca	Jun. 30, 2013 Collaborations AstraZeneca	Jun. 30, 2013 Collaborations AstraZeneca	Jun. 30, 2013 Collaborations AstraZeneca Maximum item	Jun. 30, 2013 Collaborations AstraZeneca Pre-specified events	Jun. 30, 2013 Collaborations AstraZeneca Pre-specified events ISIS-STAT3	Jun. 30, 2013 Collaborations AstraZeneca Development milestones	Jun. 30, 2013 Collaborations AstraZeneca Regulatory milestones	Jun. 30, 2013 Collaborations Biogen Idec	Jun. 30, 2012 Collaborations Biogen Idec	Jun. 30, 2013 Collaborations Biogen Idec	Jun. 30, 2012 Collaborations Biogen Idec	Dec. 31, 2012 Collaborations Biogen Idec item	Jan. 31, 2012 Collaborations Biogen Idec Agreement entered into in January 2012	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Phase 2/3 item	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Development milestones	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in January 2012 Regulatory milestones	Jun. 30, 2012 Collaborations Biogen Idec Agreement entered into in June 2012	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in June 2012 IND-enabling toxicology study	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in June 2012 Development milestones	Jun. 30, 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	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in December 2012 IND-enabling toxicology study	Jun. 30, 2013 Collaborations Biogen Idec Agreement entered into in December 2012 Clinical and regulatory milestones	Jun. 30, 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	Jun. 30, 2013 Collaborations Genzyme Corporation	Mar. 31, 2013 Collaborations Genzyme Corporation	Jun. 30, 2012 Collaborations Genzyme Corporation	Jun. 30, 2013 Collaborations Genzyme Corporation	Jun. 30, 2012 Collaborations Genzyme Corporation	Dec. 31, 2012 Collaborations Genzyme Corporation	Jun. 30, 2013 Collaborations Genzyme Corporation Minimum	Jun. 30, 2013 Collaborations Genzyme Corporation Maximum	Jun. 30, 2013 Collaborations Genzyme Corporation Pre-specified events	Jun. 30, 2013 Collaborations Genzyme Corporation Regulatory milestones	Jun. 30, 2013 Collaborations Genzyme Corporation Commercialization milestones	Mar. 31, 2010 Collaborations Glaxo Smith Kline item	Jun. 30, 2013 Collaborations Glaxo Smith Kline	Jun. 30, 2012 Collaborations Glaxo Smith Kline	Jun. 30, 2013 Collaborations Glaxo Smith Kline item	Jun. 30, 2012 Collaborations Glaxo Smith Kline	Dec. 31, 2012 Collaborations Glaxo Smith Kline	Dec. 31, 2012 Collaborations Glaxo Smith Kline ISIS-TTR	Jun. 30, 2013 Collaborations Glaxo Smith Kline Up to Phase 2 proof-of-concept	Jun. 30, 2013 Collaborations Glaxo Smith Kline Phase 2/3 ISIS-TTR	Jun. 30, 2013 Collaborations Glaxo Smith Kline Pre-specified events	Jun. 30, 2013 Collaborations Glaxo Smith Kline Development milestones	Jul. 31, 2013 Collaborations Glaxo Smith Kline Development milestones ISIS-TTR	Feb. 28, 2013 Collaborations Glaxo Smith Kline Development milestones ISIS-TTR	Jun. 30, 2013 Collaborations Glaxo Smith Kline Pre-licensing milestones Phase 2/3 ISIS-TTR	Jun. 30, 2013 Collaborations Glaxo Smith Kline Regulatory milestones	Jun. 30, 2013 Collaborations Glaxo Smith Kline Commercialization milestones	Apr. 30, 2013 Collaborations Roche	Jun. 30, 2013 Collaborations Roche	Jun. 30, 2013 Collaborations Roche	Jun. 30, 2013 Collaborations Roche Drug targeting HTT protein	Jun. 30, 2013 Collaborations Roche Pre-specified events Drug targeting HTT protein	Jun. 30, 2013 Collaborations Roche Development milestones Drug targeting HTT protein	Jun. 30, 2013 Collaborations Roche Development milestones Additional drugs	Jun. 30, 2013 Collaborations Roche Regulatory milestones Drug targeting HTT protein	Jun. 30, 2013 Collaborations Roche Commercialization milestones Drug targeting HTT protein	Jun. 30, 2013 Collaborations Roche Commercialization milestones Drug using Roche's proprietary brain shuttle technology	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc.	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc.	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Phase 2	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Pre-specified events item	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Development milestones	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Regulatory milestones	Jun. 30, 2013 Collaborations Xenon Pharmaceuticals Inc. Agreement entered into in November 2010 Commercialization milestones	Apr. 30, 2013 Collaborations CHDI Foundation, Inc.	Jun. 30, 2013 Collaborations CHDI Foundation, Inc.	Jun. 30, 2013 Collaborations CHDI Foundation, Inc.
Collaborations
Number of targets							5																						3
Upfront and near-term payments							$ 31,000,000
Upfront fee received						6,000,000	25,000,000			31,000,000											29,000,000				12,000,000				30,000,000																								2,500,000										30,000,000
Number of programs under which drugs are to be developed											3
Number of collaborations																				3
License fee received																																			175,000,000
Equity investment in entity made by strategic alliance partner	173,200,000			173,223,000																															150,000,000
Equity investment in entity made by strategic alliance partner (in shares)	9,617,869																																		5,000,000
Profit share as percentage of commercial sales																																										30.00%	50.00%
Maximum number of programs under strategic alliance																																															6			5
Milestone payment recognized				46,000,000		10,000,000										3,500,000																	25,000,000				25,000,000																					2,000,000	7,500,000
Cumulative milestone payments earned under collaborative arrangement at period end																3,500,000		3,500,000																																								19,500,000
Maximum amount of payments receivable												970,000,000		315,500,000	655,000,000								45,000,000	150,000,000			59,000,000	130,000,000																1,500,000,000	700,000,000	825,000,000										1,200,000,000	202,500,000			48,000,000	526,500,000	445,000,000					362,000,000	67,000,000		170,000,000	80,000,000	50,000,000						296,000,000	26,000,000	150,000,000	120,000,000
Number of milestone payments																						4
Next prospective milestone													50,000,000									18,000,000				10,000,000				10,000,000									25,000,000																2,000,000											22,000,000											3,000,000
Next prospective milestone payment under amended terms																						2,000,000
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%			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
Research and development revenue recognized		37,615,000	47,140,000	79,535,000	68,957,000																																																																							1,500,000
License fee recognized		477,000	200,000	1,916,000	1,618,000	2,200,000	9,300,000																																																																				2,000,000	2,000,000
Convertible promissory note repaid by Xenon																																																																											1,500,000
Revenue earned		38,092,000	47,340,000	81,451,000	70,575,000			15,300,000	17,800,000							7,400,000	1,800,000	11,200,000	3,600,000																	7,500,000		42,800,000	32,500,000	59,100,000								2,300,000	2,000,000	12,200,000	4,000,000													1,300,000	1,300,000								3,500,000	3,500,000									122,000	414,000
Percent of total revenue								40.00%	22.00%							19.00%		14.00%																		20.00%			40.00%									6.00%		15.00%
Deferred revenue						15,400,000	15,700,000	15,400,000	15,400,000	15,400,000						55,900,000		55,900,000		62,600,000																3,800,000			3,800,000		3,800,000							15,400,000		15,400,000		19,900,000												28,800,000	28,800,000
Average maximum milestone payments receivable per program																																																						20,000,000
Expense reimbursement paid																																																																																		1,500,000
Expected future reimbursement payments																																																																																				$ 1,500,000
Number of independent products required to achieve pre-specified milestone events																																																																														2