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

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

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|                                                                |  |
| Delaware                                                       | 94-2359345 |
| (State or other jurisdiction of incorporation or organization) | (I.R.S. Employer Identification Number) |
|                                                           |   |
| 3100 Hansen Way, Palo Alto, California                         | 94304-1038 |
| (Address of principal executive offices)                       | (Zip Code) |

|                            |
|----------------------------|
|                            |  |  |
| Title of each class        |   | Name of each exchange on which registered |
| Common Stock, $1 par value |   | New York Stock Exchange |

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|--------|
|        |  |  |  |  |  |  |
|   | Large accelerated filer x |    | Accelerated filer o |
|   |   |   |   |   |
|   | Non-accelerated filer o |    | Smaller reporting company o |
|   |   |   |   |
|   | (Do not check if a smaller reporting company) |    |   |   |   |

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|        |  |  |
|   |   | VARIAN MEDICAL SYSTEMS, INC. |
|   |   |
| By:    |   | /s/ Elisha W. Finney |
|   |   | Elisha W. FinneyExecutive Vice President, Finance andChief Financial Officer |

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|               |
|---------------|
|               |  |  |
| ExhibitNumber |   | Description |
|          |   |   |
| 2             |   | Amended and Restated Distribution Agreement, dated as of January 14, 1999, by and among Varian Associates, Inc. (which has been renamed Varian Medical Systems, Inc.), Varian, Inc. and Varian Semiconductor Equipment Associates, Inc. (incorporated by reference to Exhibit No. 2 to the Registrant’s Form 8-K Current Report filed as of April 2, 1999, File No. 1-7598). |
|          |   |   |
| 3.1           |   | Registrant’s Amended and Restated Certificate of Incorporation, as amended (incorporated by reference to Exhibit No. 3.1 to the Registrant’s Form 8-K Current Report filed as of August 18, 2014, File No. 1-7598). |
|          |   |   |
| 3.2           |   | Registrant’s By-Laws, as amended, effective August 18, 2014 (incorporated by reference to Exhibit No. 3.2 to the Registrant’s Form 8-K Current Report filed as of August 18, 2014, File No. 1-7598). |
|          |   |   |
| 4.1           |   | Specimen Common Stock Certificate (incorporated by reference to Exhibit No. 4.1 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended April 2, 1999, File No. 1-7598). |
|          |   |   |
| 10.1†   |   | Form of Registrant’s Indemnity Agreement with the directors and executive officers (incorporated by reference to Exhibit No. 10.3 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended April 2, 1999, File No. 1-7598). |
|          |   |   |
| 10.2†*  |   | Form of Registrant’s Change in Control Agreement for Chief Executive Officer. |
|          |   |   |
| 10.3†*  |   | Form of Registrant’s Change in Control Agreement for Senior Executives (Chief Financial Officer and General Counsel). |
|          |   |   |
| 10.4†*  |   | Form of Registrant’s Change in Control Agreement for Senior Executives (other than the Chief Executive Officer, the Chief Financial Officer, and the General Counsel). |
|          |   |   |
| 10.5†*  |   | Form of Registrant’s Change in Control Agreement for Key Employees. |
|          |   |   |
| 10.6          |   | Amended and Restated Note Purchase and Private Shelf Agreement, dated as of April 2, 1999, between the Registrant and Prudential Insurance Company of America (certain exhibits and schedules omitted) (incorporated by reference to Exhibit No. 10.7 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended April 2, 1999, File No. 1-7598). |
|          |   |   |
| 10.7          |   | Employee Benefits Allocation Agreement, dated April 2, 1999, by and among Varian Associates, Inc. (which has been renamed Varian Medical Systems, Inc.), Varian, Inc. and Varian Semiconductor Equipment Associates, Inc. (incorporated by reference to Exhibit No. 99.1 to the Registrant’s Form 8-K Current Report filed as of April 2, 1999, File No. 1-7598). |
|          |   |   |
| 10.8          |   | Intellectual Property Agreement, dated April 2, 1999, by and among Varian Associates, Inc. (which has been renamed Varian Medical Systems, Inc.), Varian, Inc. and Varian Semiconductor Equipment Associates, Inc. (incorporated by reference to Exhibit No. 99.2 to the Registrant’s Form 8-K Current Report filed as of April 2, 1999, File No. 1-7598). |
|          |   |   |
| 10.9          |   | Tax Sharing Agreement, dated April 2, 1999, by and among Varian Associates, Inc. (which has been renamed Varian Medical Systems, Inc.), Varian, Inc. and Varian Semiconductor Equipment Associates, Inc. (incorporated by reference to Exhibit No. 99.3 to the Registrant’s Form 8-K Current Report filed as of April 2, 1999, File No. 1-7598). |
|          |   |   |
| 10.10†  |   | Registrant’s Frozen Deferred Compensation Plan (incorporated by reference to Exhibit No. 10.17 to the Registrant’s Form 10-K Annual Report for the fiscal year ended September 29, 2000, File No. 1-7598). |
|          |   |   |
| 10.11†  |   | Registrant’s Amended and Restated 2005 Deferred Compensation Plan (incorporated by reference to Exhibit No. 10.2 of the Registrant’s Form 10-Q Quarterly Report for the quarter ended January 2, 2009, File No. 1-7598). |

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|               |
|---------------|
|               |  |  |  |  |
| ExhibitNumber |   | Description |
|          |   |   |
| 10.12†* |   | Registrant’s Management Incentive Plan. |
|          |   |   |
| 10.13†  |   | Registrant’s Retirement Plan (incorporated by reference to Exhibit No. 99.1 to the Registrant’s Registration Statement on Form S-8 filed on March 14, 2001, and amended June 20, 2001, Registration No. 333-57012). |
|          |   |   |
| 10.14†  |   | Registrant’s 2010 Employee Stock Purchase Plan (incorporated by reference to Exhibit No. 10.1 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended April 2, 2010, File No. 1-7598). |
|          |   |   |
| 10.15†* |   | Description of Certain Compensatory Arrangements between the Registrant and its Executive Officers and Directors as of November 20, 2015. |
|          |   |   |
| 10.16†  |   | Registrant’s Second Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.1 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2007, File No. 1-7598). |
|          |   |   |
| 10.17†  |   | Amendment No. 3 to the Registrant’s Second Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.4 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended April 3, 2009, File No. 1-7598). |
|          |   |   |
| 10.18†  |   | Form of Registrant’s Nonqualified Stock Option Agreement under the Registrant’s Second Amended and Restated 2005 Omnibus Stock Plan (effective for nonqualified stock option awards) (incorporated by reference to Exhibit No. 10.22 to the Registrant’s Form 10-K Annual Report for the fiscal year ended September 28, 2007, File No. 1-7598). |
|          |   |   |
| 10.19†  |   | Form of Registrant’s Nonqualified Stock Option Agreement under the Registrant’s Second Amended and Restated 2005 Omnibus Stock Plan (effective for nonqualified stock option awards granted to executive officers) (incorporated by reference to Exhibit No. 10.23 to the Registrant’s Form 10-K Annual Report for the fiscal year ended September 28, 2007, File No. 1-7598). |
|          |   |   |
| 10.20†  |   | Form of Registrant’s Nonqualified Stock Option Agreement under the Registrant’s Second Amended and Restated 2005 Omnibus Stock Plan (effective for nonqualified stock option awards granted to non-employee directors) (incorporated by reference to Exhibit No. 10.24 to the Registrant’s Form 10-K Annual Report for the fiscal year ended September 28, 2007, File No. 1-7598). |
|          |   |   |
| 10.21†  |   | Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.1 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.22†  |   | Form of Registrant’s Nonqualified Stock Option Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.2 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.23†  |   | Form of Registrant’s Nonqualified Stock Option Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (effective for nonqualified stock option awards granted to executive officers after November 8, 2015) (incorporated by reference to Exhibit No. 10.1 to the Registrant’s Form 8-K Current Report filed as of November 12, 2015, File No. 1-7598). |
|          |   |   |
| 10.24†  |   | Form of Registrant’s Non-Employee Director Nonqualified Stock Option Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Option Plan (incorporated by reference to Exhibit No. 10.3 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.25†  |   | Form of Registrant’s Non-Employee Director Nonqualified Stock Option Agreement (for use in Singapore) under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit 10.4 of the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.26†  |   | Form of Registrant’s Non-Employee Director Nonqualified Stock Option Agreement (for use outside of U.S. except for Singapore) under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.26 to the Registrant’s Form 10-K Annual Report for the year ended September 28, 2012, File No. 1-7598). |

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|               |
|---------------|
|               |  |  |  |  |
| ExhibitNumber |   | Description |
|          |   |   |
| 10.27†  |   | Form of Registrant’s Restricted Stock Unit Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.5 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.28†  |   | Form of Registrant’s Restricted Stock Unit Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (effective for restricted stock unit awards granted to executive officers on or after October 1, 2013 and prior to November 9, 2015) (incorporated by reference to Exhibit No. 10.2 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended December 27, 2013, File No. 1-7598). |
|          |   |   |
| 10.29†  |   | Form of Registrant’s Restricted Stock Unit Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (effective for restricted stock unit awards granted to executive officers after November 8, 2015) (incorporated by reference to Exhibit No. 10.2 to the Registrant’s Form 8-K Current Report filed as of November 12, 2015, File No. 1-7598). |
|          |   |   |
| 10.30†* |   | Form of Registrant’s Performance Unit Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan. |
|          |   |   |
| 10.31†* |   | Form of Registrant’s Performance Unit Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (effective for performance unit awards granted to executive officers on or after October 1, 2013 and prior to November 9, 2015). |
|          |   |   |
| 10.32†  |   | Form of Registrant’s Performance Unit Agreement under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (effective for performance unit awards granted to executive officers after November 8, 2015) (incorporated by reference to Exhibit No. 10.3 to the Registrant’s Form 8-K Current Report filed as of November 12, 2015, File No. 1-7598). |
|          |   |   |
| 10.33†  |   | Form of Registrant’s Grant Agreement for Deferred Stock Units under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.7 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.34†  |   | Form of Registrant’s Non-Employee Grant Agreement for Deferred Stock Units (for use in Singapore) under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit 10.8 of the Registrant’s Form 10-Q Quarterly Report for the quarter ended March 30, 2012, File No. 1-7598). |
|          |   |   |
| 10.35†  |   | Form of Registrant’s Non-Employee Grant Agreement for Deferred Stock Units (for use outside of U.S. except for Singapore) under the Registrant’s Third Amended and Restated 2005 Omnibus Stock Plan (incorporated by reference to Exhibit No. 10.31 to the Registrant’s Form 10-K Annual Report for the year ended September 28, 2012, File No. 1-7598). |
|          |   |   |
| 10.36         |   | Credit Agreement, dated as of August 27, 2013, among the Registrant, Bank of America, N.A., as Administrative Agent, Swing Line Lender and L/C Issuer and each lender from time to time party thereto (incorporated by reference to Exhibit No. 10.32 to the Registrant’s Form 10-K Annual Report for the year ended September 26, 2014, File No. 1-7598). |
|          |   |   |
| 10.37         |   | Amendment No. 1, effective as of September 27, 2013, to the Credit Agreement, dated as of August 27, 2013, among the Registrant, Bank of America, N.A., as Administrative Agent, Swing Line Lender and L/C Issuer and each of the lenders signatory thereto (incorporated by reference to Exhibit No. 10.1 to the Registrant’s Form 10-Q Quarterly Report for the quarter ended December 27, 2013, File No. 1-7598). |
|          |   |   |
| 10.38         |   | Loan and Security Agreement between California Proton Treatment Center, LLC, ORIX Capital Markets, LLC, ORIX Capital Markets, LLC, and Varian Medical Systems International AG, dated September 30, 2011 (incorporated by reference to Exhibit No. 10.44 to the Registrant’s Form 10-K Annual Report for the fiscal year ended September 30, 2011, File No. 1-7598). |
|          |   |   |
| 10.39*        |   | First Amendment to Loan and Security Agreement and Other Loan Documents among ORIX Capital Markets, LLC, California Proton Treatment Center, LLC and Jeffrey L. Bordox and James Thomson, dated as of October 25, 2013. |

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|               |
|---------------|
|               |  |  |
| ExhibitNumber |   | Description |
|          |   |   |
| 10.40*        |   | Second Amendment to Loan and Security Agreement and Other Loan Documents among ORIX Capital Markets, LLC, ORIX Capital Markets, LLC, and Varian Medical Systems International AG, dated as of June 10, 2014. |
|          |   |   |
| 10.41*        |   | Third Amendment to Loan and Security Agreement and Other Loan Documents And Amendment to Fee Deed of Trust and Leasehold Deed of Trust among ORIX Capital Markets, LLC, ORIX Capital Markets, LLC, Varian Medical Systems International AG, and JP Morgan Chase Bank, N.A., dated as of November 6, 2015. |
|          |   |   |
| 10.42         |   | Revenue Sharing Agreement between ORIX Proton San Diego, LLC and Varian Medical Systems International AG, dated September 30, 2011 (incorporated by reference to Exhibit No. 10.45 to the Registrant’s Form 10-K Annual Report for the fiscal year ended September 30, 2011, File No. 1-7598). |
|          |   |   |
| 10.43**++     |   | Loan and Security Agreement (Building Loan) dated as of July 15, 2015 by and among MM PROTON I, LLC, as Borrower; JPMORGAN CHASE BANK, N.A., as Administrative Agent and Collateral Agent; and the Lenders referenced therein.  “Lenders” includes the Registrant. |
|          |   |   |
| 10.44**++     |   | First Amendment to Loan and Security Agreement (Building Loan) dated as of August 5, 2015 by and among MM PROTON I, LLC, as Borrower; JPMORGAN CHASE BANK, N.A., as Administrative Agent and Collateral Agent; and the Lenders referenced therein. “Lenders” includes the Registrant. |
|          |   |   |
| 10.45**++     |   | Loan and Security Agreement (Project Loan) dated as of July 15, 2015 by and among MM PROTON I, LLC, a Borrower; JPMORGAN CHASE BANK, N.A., as Administrative Agent and Collateral Agent, and the Lenders referenced therein. “Lenders” includes the Registrant. |
|          |   |   |
| 10.46**++     |   | Amendment No. One to Loan and Security Agreement (Project Loan) dated as of July 31, 2015 by and among MM PROTON I, LLC, as Borrower; JPMORGAN CHASE BANK, N.A., as Administrative Agent and Collateral Agent, and the Lenders referenced therein. “Lenders” includes the Registrant. |
|          |   |   |
| 21*           |   | List of Subsidiaries as of November 1, 2015. |
|          |   |   |
| 23*           |   | Consent of Independent Registered Public Accounting Firm. |
|          |   |   |
| 31.1*         |   | Chief Executive Officer Certification Pursuant to Rule 13a-14(a) of the Securities Exchange Act. |
|          |   |   |
| 31.2*         |   | Chief Financial Officer Certification Pursuant to Rule 13a-14(a) of the Securities Exchange Act. |
|          |   |   |
| 32.1*         |   | Certification pursuant to 18 U.S.C. Section 1350 as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. |
|          |   |   |
| 32.2*         |   | Certification pursuant to 18 U.S.C. Section 1350 as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. |
|          |   |   |
| 101.INS       |   | XBRL Instance Document |
|          |   |   |
| 101.SCH       |   | XBRL Taxonomy Extension Schema Document |
|          |   |   |
| 101.CAL       |   | XBRL Taxonomy Extension Calculation Linkbase Document |
|          |   |   |
| 101.DEF       |   | XBRL Taxonomy Extension Definition Linkbase Document |
|          |   |   |
| 101.LAB       |   | XBRL Taxonomy Extension Label Linkbase Document |
|          |   |   |
| 101.PRE       |   | XBRL Taxonomy Extension Presentation Linkbase Document |

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|         |  |
| † | Management contract or compensatory arrangement. |
|    |   |
| *       | Previously filed |
|    |   |
| **      | Filed herewith |
|    |   |
| ++      | Confidential treatment has been requested as to certain portions of this exhibit pursuant to Rule 24b-2 of the Securities Exchange Act of 1934, as amended. |

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