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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 |  |  |  |  |  |

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