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Segment Information and Concentration of Business Risk, Segment Information (Details)
$ in Thousands
3 Months Ended 9 Months Ended
Sep. 30, 2016
USD ($)
Sep. 30, 2015
USD ($)
Sep. 30, 2016
USD ($)
Segment
Sep. 30, 2015
USD ($)
Dec. 31, 2015
USD ($)
Segment Information and Concentration of Business Risk [Abstract]          
Number of reportable segments | Segment     2    
Revenue [Abstract]          
Research and development $ 108,913 $ 48,918 $ 166,583 $ 230,469  
Licensing and royalty 2,014 203 19,689 1,664  
Total revenue 110,927 49,121 186,272 232,133  
Income (loss) from operations 16,108 (48,138) (87,471) (12,821)  
Total assets 843,586   843,586   $ 947,900
Operating Segments [Member] | Ionis Core [Member]          
Revenue [Abstract]          
Research and development 112,761 50,511 170,431 232,062  
Licensing and royalty 2,014 203 19,689 1,664  
Total revenue 114,775 50,714 190,120 233,726  
Income (loss) from operations 36,328 (35,067) (36,465) 16,323  
Total assets 931,231   931,231   994,191
Operating Segments [Member] | Akcea Therapeutics [Member]          
Revenue [Abstract]          
Research and development 0 0 0 0  
Licensing and royalty 0 0 0 0  
Total revenue 0 0 0 0  
Income (loss) from operations (20,250) (13,101) (51,096) (29,054)  
Total assets 62,009   62,009   66,068
Elimination of Intercompany Activity [Member]          
Revenue [Abstract]          
Research and development (3,848) (1,593) (3,848) (1,593)  
Licensing and royalty 0 0 0 0  
Total revenue (3,848) (1,593) (3,848) (1,593)  
Income (loss) from operations 30 $ 30 90 $ (90)  
Total assets $ (149,654)   $ (149,654)   $ (112,359)