CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (Unaudited) - USD ($) shares in Thousands, $ in Thousands	Common Stock [Member]	Additional Paid In Capital [Member]	Accumulated Other Comprehensive Loss [Member]	Accumulated Deficit [Member]	Total Ionis Stockholders' Equity [Member]	Noncontrolling Interest in Akcea Therapeutics, Inc. [Member]	Total
Balance at Dec. 31, 2017	$ 125	$ 1,553,681	$ (31,759)	$ (1,241,034)	$ 281,013	$ 84,267	$ 365,280
Balance (in shares) at Dec. 31, 2017	124,976
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	(46,335)	(46,335)	0	(46,335)
Change in unrealized gains (losses), net of tax	0	0	(834)	0	(834)	0	(834)
Foreign currency translation	0	0	61	0	61	0	61
Biogen stock purchase	$ 11	447,954	0	0	447,965	0	447,965
Biogen stock purchase (in shares)	11,502
Issuance of common stock in connection with employee stock plans	$ 2	14,800	0	0	14,802	0	14,802
Issuance of common stock in connection with employee stock plans (in shares)	1,029
Stock-based compensation expense	$ 0	97,210	0	0	97,210	0	97,210
Noncontrolling interest in Akcea Therapetuics, Inc.	0	(83,332)	0	0	(83,332)	45,327	(38,005)
Balance at Sep. 30, 2018	$ 138	2,030,313	(32,532)	(1,287,369)	710,550	129,594	840,144
Balance (in shares) at Sep. 30, 2018	137,507
Balance at Jun. 30, 2018	$ 137	2,011,561	(32,634)	(1,282,810)	696,254	121,181	817,436
Balance (in shares) at Jun. 30, 2018	137,157
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	(4,559)	(4,559)	0	(4,559)
Change in unrealized gains (losses), net of tax	0	0	133	0	133	0	133
Foreign currency translation	0	0	(31)	0	(31)	0	(31)
Issuance of common stock in connection with employee stock plans	$ 1	6,225	0	0	6,226	0	6,226
Issuance of common stock in connection with employee stock plans (in shares)	350
Stock-based compensation expense	$ 0	34,883	0	0	34,883	0	34,883
Noncontrolling interest in Akcea Therapetuics, Inc.	0	(22,356)	0	0	(22,356)	8,413	(13,943)
Balance at Sep. 30, 2018	$ 138	2,030,313	(32,532)	(1,287,369)	710,550	129,594	840,144
Balance (in shares) at Sep. 30, 2018	137,507
Balance at Dec. 31, 2018	$ 138	2,047,250	(32,016)	(967,293)	1,048,079	139,081	1,187,160
Balance (in shares) at Dec. 31, 2018	137,929
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	109,730	109,730	0	109,730
Change in unrealized gains (losses), net of tax	0	0	6,666	0	6,666	0	6,666
Foreign currency translation	0	0	(25)	0	(25)	0	(25)
Issuance of common stock in connection with employee stock plans	$ 3	112,132	0	0	112,135	0	112,135
Issuance of common stock in connection with employee stock plans (in shares)	2,855
Stock-based compensation expense	$ 0	111,564	0	0	111,564	0	111,564
Payments of tax withholdings related to vesting of share-based awards and exercise of employee stock options	$ 0	(18,841)	0	0	(18,841)	0	(18,841)
Payments of tax withholdings related to vesting of share-based awards and exercise of employee stock options (in shares)	(147)
Noncontrolling interest in Akcea Therapetuics, Inc.	$ 0	(33,015)	0	0	(33,015)	22,592	(10,423)
Balance at Sep. 30, 2019	$ 141	2,219,090	(25,375)	(857,563)	1,336,293	161,673	1,497,966
Balance (in shares) at Sep. 30, 2019	140,637
Balance at Jun. 30, 2019	$ 140	2,177,222	(24,252)	(883,726)	1,269,384	187,818	1,457,202
Balance (in shares) at Jun. 30, 2019	140,393
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	26,163	26,163	0	26,163
Change in unrealized gains (losses), net of tax	0	0	(1,110)	0	(1,110)	0	(1,110)
Foreign currency translation	0	0	(13)	0	(13)	0	(13)
Issuance of common stock in connection with employee stock plans	$ 1	10,130	0	0	10,131	0	10,131
Issuance of common stock in connection with employee stock plans (in shares)	255
Stock-based compensation expense	$ 0	24,126	0	0	24,126	0	24,126
Payments of tax withholdings related to vesting of share-based awards and exercise of employee stock options	$ 0	(10,804)	0	0	(10,804)	0	(10,804)
Payments of tax withholdings related to vesting of share-based awards and exercise of employee stock options (in shares)	(11)
Noncontrolling interest in Akcea Therapetuics, Inc.	$ 0	18,416	0	0	18,416	(26,145)	(7,729)
Balance at Sep. 30, 2019	$ 141	$ 2,219,090	$ (25,375)	$ (857,563)	$ 1,336,293	$ 161,673	$ 1,497,966
Balance (in shares) at Sep. 30, 2019	140,637