Annual Meeting

2017 Annual Meeting

Ionis Pharmaceuticals, Inc. (the “Company”) held its Annual Meeting of Stockholders on May 24, 2017. The stockholders considered five proposals, each of which is described in more detail in the Company’s definitive proxy statement dated April 6, 2017.

Proposal 1:

Election of directors to hold office until the 2020 Annual Meeting:

FOR

WITHHELD

BROKER
NON-VOTES

Spencer R. Berthelsen

84,173,655

9,020,996

21,105,539

B. Lynne Parshall

87,494,494

5,700,157

21,105,539

Joseph H. Wender

84,148,943

9,045,708

21,105,539

The Company’s stockholders elected the foregoing candidates, by affirmative votes by a majority of the votes of the shares.

Proposal 2:

Approve an amendment to the Ionis Pharmaceuticals, Inc. 2011 Equity Incentive Plan:

FOR

AGAINST

ABSTAIN

BROKER NON-VOTES

81,668,509

11,359,170

166,972

21,105,539

The Company’s stockholders approved the foregoing proposal.

Proposal 3:

Approval, on an advisory basis, of the compensation paid to the Company’s executive officers, including the following resolution:

“RESOLVED, that Ionis’ stockholders approve, on an advisory basis, the compensation of the named executive officers, as disclosed in this Proxy Statement for the 2017 Annual Meeting of Stockholders pursuant to the compensation disclosure rules of the Securities and Exchange Commission.”

FOR

AGAINST

ABSTAIN

BROKER NON-VOTES

59,649,475

33,275,149

270,027

21,105,539

The Company’s stockholders approved the foregoing proposal.

Proposal 4:

Approval, on an advisory basis, of the frequency of holding an advisory vote on executive compensation:

FOR

AGAINST

ABSTAIN

BROKER NON-VOTES

92,187,838

272,627

624,013

110,173

Based on the results of this vote, and consistent with the recommendation of the Company’s Board of Directors, the Company will hold an advisory vote on executive compensation on an annual basis until the next required vote on the frequency of holding such an advisory vote, which is required at least once every six years.

Proposal 5:

Ratify the Audit Committee's selection of Ernst & Young LLP as independent auditors for our 2017 fiscal year:

FOR

AGAINST

ABSTAIN

BROKER NON-VOTES

112,038,206

2,075,791

186,193

0

The Company’s stockholders approved the foregoing proposal.

2016 Annual Meeting

Ionis Pharmaceuticals, Inc. (the “Company”) held its Annual Meeting of Stockholders on June 3, 2016. The stockholders considered three proposals, each of which is described in more detail in the Company’s definitive proxy statement dated April 15, 2016.

Proposal 1:

Election of directors to hold office until the 2019 Annual Meeting:

FOR

WITHHELD

BROKER
NON-VOTES

Stanley T. Crooke

74,787,512

5,029,186

21,563,698

Joseph Klein, III

78,504,840

1,311,858

21,563,698

Joseph Loscalzo

76,326,735

3,489,963

21,563,698

The Company’s stockholders elected the foregoing candidates, by affirmative votes by a majority of the votes of the shares represented in person or by proxy at the meeting and entitled to vote in the election of directors.

Proposal 2:

Approve an amendment to the Isis Pharmaceuticals, Inc. 2011 Equity Incentive Plan.

"RESOLVED, that Ionis’ stockholders approve, on an advisory basis, the compensation of the named executive officers, as disclosed in this Proxy Statement for the 2016 Annual Meeting of Stockholders pursuant to the compensation disclosure rules of the Securities and Exchange Commission."

FOR

AGAINST

ABSTAIN

BROKER NON-VOTES

77,717,101

1,886,818

212,779

21,563,698

The Company’s stockholders approved the foregoing proposal.

Proposal 3:

Ratify the Audit Committee's selection of Ernst & Young LLP as independent auditors for our 2016 fiscal year:

FOR

AGAINST

ABSTAIN

BROKER NON-VOTES

100,224,042

898,993

257,361

0

The Company’s stockholders approved the foregoing proposal.