FORM 4
[ ] Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).         
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP OF SECURITIES
                                                                                  
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Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934 or Section 30(h) of the Investment Company Act of 1940
                      

1. Name and Address of Reporting Person *

O'NEIL PATRICK R. 		2. Issuer Name and Ticker or Trading Symbol

IONIS PHARMACEUTICALS INC [ IONS ] 		5. Relationship of Reporting Person(s) to Issuer (Check all applicable)

_____ Director                      _____ 10% Owner
__ X __ Officer (give title below)      _____ Other (specify below)
SVP, Legal & General Counsel
(Last)          (First)          (Middle)

C/O IONIS PHARMACEUTICALS, INC., 2855 GAZELLE COURT 		3. Date of Earliest Transaction (MM/DD/YYYY)

1/15/2017
(Street)

CARLSBAD, CA 92010
(City)        (State)        (Zip)
4. If Amendment, Date Original Filed (MM/DD/YYYY)

 
6. Individual or Joint/Group Filing (Check Applicable Line)

_ X _ Form filed by One Reporting Person
___ Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security
(Instr. 3) 		2. Trans. Date 2A. Deemed Execution Date, if any 3. Trans. Code
(Instr. 8) 		4. Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4 and 5) 		5. Amount of Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 3 and 4) 		6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4)
Code V Amount (A) or (D) Price
Common Stock   1/15/2017   1/15/2017   M (1)    312   (1) A $0   10262   D  
 
Common Stock   1/17/2017   1/17/2017   S (2)    122   (2) D $46.293   10140   D  
 
Common Stock   1/15/2017   1/15/2017   M (1)    653   (1) A $0   10793   D  
 
Common Stock   1/17/2017   1/17/2017   S (2)    256   (2) D $46.29   10537   D  
 
Common Stock   1/15/2017   1/15/2017   M (3)    1875   (3) A $0   12412   D  
 
Common Stock   1/17/2017   1/17/2017   S (4)    733   (4) D $46.29   11679   D  
 
Common Stock   1/15/2017   1/15/2017   M (5)    1311   (5) A $0   12990   D  
 
Common Stock   1/17/2017   1/17/2017   S (6)    512   (6) D $46.291   12478   D  
 
Common Stock   1/15/2017   1/15/2017   M (7)    1594   (7) A $0   14072   D  
 
Common Stock   1/17/2017   1/17/2017   S (8)    623   (8) D $46.29   13449   D  
 

Table II - Derivative Securities Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities)
1. Title of Derivate Security
(Instr. 3) 		2. Conversion or Exercise Price of Derivative Security 3. Trans. Date 3A. Deemed Execution Date, if any 4. Trans. Code
(Instr. 8) 		5. Number of Derivative Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4 and 5) 		6. Date Exercisable and Expiration Date 7. Title and Amount of Securities Underlying Derivative Security
(Instr. 3 and 4) 		8. Price of Derivative Security
(Instr. 5) 		9. Number of derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4)
Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares
Restricted Stock Units     (9) 1/15/2017   1/15/2017   A      7537         (10)   (10) Common Stock   7537   $0   7537   D  
 
Restricted Stock Units     (9) 1/15/2017   1/15/2017   M         312   (2)     (11)   (11) Common Stock   312   $0   0   D  
 
Restricted Stock Units     (9) 1/15/2017   1/8/2017   M         653   (2)     (11)   (11) Common Stock   653   $0   0   D  
 
Restricted Stock Units     (9) 1/15/2017   1/15/2017   M         1875   (4)     (11)   (11) Common Stock   1875   $0   1875   D  
 
Restricted Stock Units     (9) 1/15/2017   1/15/2017   M         1311   (6)     (11)   (11) Common Stock   1311   $0   2620   D  
 
Restricted Stock Units     (9) 1/15/2017   1/15/2017   M         1594   (8)     (11)   (11) Common Stock   1594   $0   4779   D  
 

Explanation of Responses:
( 1)  Acquired pursuant to vesting and release of shares pursuant to a Restricted Stock Unit award granted on January 15, 2013.
( 2)  The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 15, 2013.
( 3)  Acquired pursuant to vesting and release of shares pursuant to a Restricted Stock Unit award granted on January 15, 2014.
( 4)  The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 15, 2014.
( 5)  Acquired pursuant to vesting and release of shares pursuant to a Restricted Stock Unit award granted on January 15, 2015.
( 6)  The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 15, 2015.
( 7)  Acquired pursuant to vesting and release of shares pursuant to a Restricted Stock Unit award granted on January 15, 2016.
( 8)  The sale was made pursuant to an automatic sale to cover the required tax withholding obligations pursuant to the 2011 Equity Incentive Plan Restricted Stock Unit Agreement and Grant Notice, dated January 15, 2016.
( 9)  Each Restricted Stock Unit represents a contingent right to receive one share of Ionis common stock, or its equivalent cash value.
( 10)  Grant 1/15/2017 to reporting person of Restricted Stock Units under the Ionis Pharmaceuticals, Inc. 2011 Equity Incentive Plan. Restricted Stock Units vest in four equal annual installments, the first installment vesting on January 15, 2018. Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company. The RSU shall be fully vested on January 15, 2021. The RSU is vested as to 0 shares on January 15, 2017.
( 11)  Restricted Stock Units vest in four equal annual installments. Upon vesting, the restricted stock units will be paid out in whole shares of Ionis common stock or cash as may be determined by the Company.

Reporting Owners
Reporting Owner Name / Address
Relationships
Director 10% Owner Officer Other
O'NEIL PATRICK R.
C/O IONIS PHARMACEUTICALS, INC.
2855 GAZELLE COURT
CARLSBAD, CA 92010

SVP, Legal & General Counsel

Signatures
/s/B. Lynne Parshall, attorney-in-fact 1/18/2017
** Signature of Reporting Person Date


Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* If the form is filed by more than one reporting person, see Instruction 4(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, see Instruction 6 for procedure.
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