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Organization and Significant Accounting Policies, Basic and Diluted Net Income per Share (Details) - USD ($)
$ / shares in Units, shares in Thousands, $ in Thousands
 3 Months Ended 6 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
Jun. 30, 2017
Dec. 31, 2019
Dec. 31, 2018
Dec. 31, 2017
Basic Net Income per Share [Abstract]                        
Basic net income (loss) 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
Net income (loss) $ 184,415 $ 26,163 $ (876) $ 84,443 $ 320,078 $ (4,559) $ (40,358) $ (1,420)   $ 294,146 $ 273,741 $ 346
Net income 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
Shares used in computing basic net income 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
Income available to Ionis common shareholders, plus assumed conversions $ 196,485 $ 26,158   $ 87,543 $ 330,439         $ 296,563 $ 276,868 $ 18,792
Shares issuable related to our Employee Stock Purchase Plan (in shares)                   18 6 4
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
Diluted net income 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
Stock Options [Member]                        
Basic Net Income per Share [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]                        
Basic Net Income per Share [Abstract]                        
Shares issuable related to stock-based compensation (in shares) 848 844   665 636         766 514 459
Ionis [Member]                        
Basic Net Income per Share [Abstract]                        
Net income (loss) $ 121,552 $ 49,930 $ 27,311 $ 63,697 $ 372,913 $ 43,226 $ 5,882 $ 18,785   $ 262,490 $ 440,806 $ 110,776
Preferred Stock [Member]                        
Basic Net Income per Share [Abstract]                        
Weighted average shares owned in Akcea (in shares)                       15,748
Basic net income (loss) per share (in dollars per share)                       $ (1.80)
Net income (loss)                       $ (28,346)
Akcea [Member]                        
Basic Net Income per Share [Abstract]                        
Net income (loss)                   $ 34,073 $ (163,938) $ (91,984)
Akcea [Member] | Common Stock [Member]                        
Basic Net Income per Share [Abstract]                        
Weighted average shares owned in Akcea (in shares)                   70,100 59,812 20,669
Basic net income (loss) per share (in dollars per share)                   $ 0.49 $ (2.74) $ (3.08)
Net income (loss)                   $ 34,073 $ (163,938) $ (63,638)
Akcea [Member] | Preferred Stock [Member]                        
Basic Net Income per Share [Abstract]                        
Dividend rate                 6.00%      
Conversion ratio                   converted into common stock on a 1:1 basis    
[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.