UNITED STATES


SECURITIES AND EXCHANGE COMMISSION


Washington, D.C. 20549


FORM 10-Q/A(Amendment No. 1)


(Mark One)


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|ý | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended April 1, 2016


or


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| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the transition period from              to

Commission File Number: 000-30235


EXELIXIS, INC.(Exact name of registrant as specified in its charter)
 Delaware04-3257395(State or other jurisdiction of incorporation or organization)(I.R.S. Employer Identification Number)


210 East Grand Ave.


South San Francisco, CA 94080


(650) 837-7000


(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)


Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days).    Yes ý No  ̈


Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes ý No  ̈


Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.


Large accelerated filerýAccelerated filer ̈Non-accelerated filer ̈(Do not check if a smaller reporting company)Smaller reporting company ̈


Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ̈ No ý


As of April 28, 2016 , there were 228,739,657 shares of the registrant’s common stock outstanding.











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EXPLANATORY NOTE





Exelixis, Inc. (the “Company”) is filing this Amendment No. 1 to its Quarterly Report on Form 10-Q for the quarterly period ended April 1, 2016 (the “Form 10-Q”) as an exhibit-only filing in response to comments received from the Securities and Exchange Commission regarding a request for confidential treatment of certain portions of Exhibits 10.3 and 10.4 originally filed with the Form 10-Q. This Amendment No. 1 to Quarterly Report on Form 10-Q/A (this “Amendment”) is being filed solely to re-file Exhibits 10.3 and 10.4. In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by our principal executive officer and principal financial officer are filed as exhibits to this Amendment.


Except as described above, this Amendment does not reflect events occurring after the filing of the original Form 10-Q and no revisions are being made pursuant to this Amendment to the Company’s financial statements or any other disclosure contained in the Form 10-Q.





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SIGNATURES


Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.


EXELIXIS, INC.September 30, 2016/s/    CHRISTOPHERJ. SENNERDateChristopher J. SennerExecutive Vice President and Chief Financial Officer(Duly Authorized Officer and Principal Financial and Accounting Officer)











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EXHIBIT INDEX TO FORM 10-Q/A


ExhibitNumberExhibit DescriptionIncorporation by ReferenceFiledHerewithFormFile NumberExhibit/AppendixReferenceFiling Date10.3*Collaboration and License Agreement dated February 29, 2016, by and between Exelixis, Inc. and Ipsen Pharma SASX10.4*Supply Agreement dated February 29, 2016, by and between Exelixis, Inc. and Ipsen Pharma SASX31.1Certification required by Rule 13a-14(a) or Rule 15d-14(a).X31.2Certification required by Rule 13a-14(a) or Rule 15d-14(a).X


*Confidential treatment requested for certain portions of this exhibit.