Item 5.07. Submission of Matters to a Vote of Security Holders.

Isis Pharmaceuticals, Inc. held its Annual Meeting of Stockholders on June 7, 2012. The stockholders considered five proposals, each of which is described in more detail in the Company's definitive proxy statement dated April 23, 2012.

Proposal 1: Election of a director to hold office until the 2015 Annual Meeting:

FOR WITHHELD
Frederick T. Muto 61,856,307 5,083,807 Broker Non-Votes: 21,326,129

The foregoing candidate was elected having received 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 and restatement of the Isis Pharmaceuticals, Inc. 2002 Non-Employee Directors' Stock Option Plan:

FOR AGAINST ABSTAIN BROKER NON-VOTES 62,826,326 3,997,455 116,333 21,326,129

The foregoing proposal was approved.

Proposal 3: Approve an extension to the term of the Isis Pharmaceuticals, Inc. Amended and Restated 1989 Stock Option Plan such that the new term will end on January 31, 2024:

FOR AGAINST ABSTAIN BROKER NON-VOTES 62,936,733 3,882,685 120,696 21,326,129

The foregoing proposal was approved.

Proposal 4: Approval, on an advisory basis, of the compensation paid to the Company's executive officers, including the following resolution:

"RESOLVED, that Isis' stockholders approve, on an advisory basis, the compensation of the named executive officers, as disclosed in this Proxy Statement for the 2012 Annual Meeting of stockholders pursuant to the compensation disclosure rules of the Securities and Exchange Commission."

FOR AGAINST ABSTAIN BROKER NON-VOTES 42,075,944 24,732,013 132,157 21,326,129

The foregoing proposal was approved.

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Proposal 5: Ratify the Audit Committee's selection of Ernst & Young LLP as independent auditors for our 2012 fiscal year:

FOR AGAINST ABSTAIN BROKER NON-VOTES 86,512,876 1,460,806 292,561 0

The foregoing proposal was approved.