Quarterly Financial Data (Unaudited) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended																12 Months Ended
	Dec. 31, 2019		Sep. 30, 2019		Jun. 30, 2019		Mar. 31, 2019		Dec. 31, 2018		Sep. 30, 2018		Jun. 30, 2018		Mar. 31, 2018		Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Quarterly Financial Data (Unaudited) [Abstract]
Revenue	$ 493,680		$ 167,892		$ 163,813		$ 297,214		$ 192,113		$ 145,395		$ 117,747		$ 144,419
Operating expenses	233,028		165,369		182,640		175,679		181,331		163,967		168,028		147,720		$ 756,716	$ 661,046	$ 483,132
Income (loss) from operations	260,652		2,523		(18,827)		121,535		10,782		(18,572)		(50,281)		(3,301)		365,883	(61,372)	31,047
Net income (loss)	203,957		18,432		(10,012)		90,884		302,735		(20,365)		(56,573)		(10,812)		303,262	214,985	(10,783)
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 184,415		$ 26,163		$ (876)		$ 84,443		$ 320,078		$ (4,559)		$ (40,358)		$ (1,420)		$ 294,146	$ 273,741	$ 346
Basic net income per share (in dollars per share)	$ 1.31	[1],[2]	$ 0.19	[1],[2]	$ (0.01)	[1],[2]	$ 0.63	[1],[2]	$ 2.32	[1],[2]	$ (0.03)	[1],[2]	$ (0.29)	[1],[2]	$ (0.01)	[1],[2]	$ 2.12	$ 2.09	$ 0.15
Diluted net income (loss) per share (in dollars per share)	$ 1.28	[2],[3]	$ 0.18	[2],[3],[4]	$ (0.01)	[2]	$ 0.62	[2],[3],[4]	$ 2.21	[2],[3]	$ (0.03)	[2]	$ (0.29)	[2]	$ (0.01)	[2]	$ 2.08	$ 2.07	$ 0.15
Income (Numerator) [Abstract]
Income (loss) available to Ionis common stockholders	$ 183,795		$ 26,158		$ (933)		$ 87,543		$ 319,694		$ (4,563)		$ (37,932)		$ (1,212)		$ 296,563	$ 276,868	$ 18,792
Income available to Ionis common shareholders, plus assumed conversions	$ 196,485		$ 26,158				$ 87,543		$ 330,439								$ 296,563	$ 276,868	$ 18,792
Shares (Denominator) [Abstract]
Shares used in computing basic net income (loss) per share (in shares)	140,583		140,551		140,247		138,582		137,699		137,346		128,712		125,330		139,998	132,320	124,016
Effect of Diluted Securities [Abstract]
Shares issuable related to our ESPP (in shares)	18		20				38		7
Shares used in computing diluted net income per share (in shares)	153,303		143,408				141,537		149,856								142,872	134,056	126,098
0.125 Percent Convertible Senior Notes [Member]
Quarterly Financial Data (Unaudited) [Abstract]
Interest rate on convertible senior notes	0.125%								0.125%								0.125%	0.125%
Income (Numerator) [Abstract]
Shares issuable related to our convertible notes	$ 644
Effect of Diluted Securities [Abstract]
Shares issuable related to our convertible notes	860
1 Percent Convertible Senior Notes [Member]
Quarterly Financial Data (Unaudited) [Abstract]
Interest rate on convertible senior notes	1.00%		1.00%				1.00%		1.00%								1.00%	1.00%
Income (Numerator) [Abstract]
Shares issuable related to our convertible notes	$ 12,046		$ 0				$ 0		$ 10,745
Effect of Diluted Securities [Abstract]
Shares issuable related to our convertible notes	9,527		0				0		10,260
Stock Options [Member]
Effect of Diluted Securities [Abstract]
Shares issuable related to stock-based compensation (in shares)	1,467		1,993				2,252		1,254								2,090	1,216	1,619
Restricted Stock Awards [Member]
Effect of Diluted Securities [Abstract]
Shares issuable related to stock-based compensation (in shares)	848		844				665		636								766	514	459
Ionis [Member]
Quarterly Financial Data (Unaudited) [Abstract]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 121,552		$ 49,930		$ 27,311		$ 63,697		$ 372,913		$ 43,226		$ 5,882		$ 18,785		$ 262,490	$ 440,806	$ 110,776
Akcea [Member]
Quarterly Financial Data (Unaudited) [Abstract]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 62,243		$ (23,772)		$ (28,244)		$ 23,846		$ (53,219)		$ (47,789)		$ (43,814)		$ (19,997)
Basic net income per share (in dollars per share)	$ 0.87		$ (0.34)		$ (0.40)		$ 0.35		$ (0.79)		$ (0.73)		$ (0.72)		$ (0.44)
Weighted average shares owned in Akcea (in shares)	71,342		70,221		70,221		68,582		67,130		65,538		60,832		45,448

[1] As discussed in Note 1, Organization and Significant Accounting Policies, we compute basic net income (loss) per share by dividing the total net income (loss) attributable to our common stockholders by our weighted-average number of common shares outstanding during the period. Our basic net income (loss) per share calculation for each of the quarters in 2019 and 2018 considered our net income for Ionis on a stand-alone basis plus our share of Akcea’s net loss for the period. To calculate the portion of Akcea’s net loss attributable to our ownership, we multiplied Akcea’s loss per share by the weighted average shares we owned in Akcea during the period. As a result of this calculation, our total net income (loss) available to Ionis common stockholders for the calculation of net income (loss) per share is different than net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders in the consolidated statements of operations.

[2] We computed net income (loss) per share independently for each of the quarters presented. Therefore, the sum of the quarterly net income (loss) per share will not necessarily equal the total for the year.

[3] We had net income available to Ionis common stockholders for the following periods. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during those periods.

[4] For the three months ended March 31, 2019 and September 30, 2019, the calculation excluded the 1 percent notes because the effect on diluted earnings per share was anti-dilutive.