UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 8-K

CURRENT REPORT

PURSUANT TO SECTION 13 OR 15(d)

OF THE SECURITIES EXCHANGE ACT OF 1934

Date of report (Date of earliest event reported): June 9, 2015

SEQUENOM, INC.

(Exact Name of Registrant as Specified in Charter)

3595 JOHN HOPKINS COURT

SAN DIEGO, CALIFORNIA 92121

(Address of Principal Executive Offices)

(858) 202-9000

(Registrant’s telephone number, including area code)

N/A

(Former name or former address, if changed since last report)

Check the appropriate box below if the Form 8-K is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions (see General Instruction A.2. below):

On June 9, 2015, Sequenom, Inc. (the “Company”) entered into an indenture, dated as of June 9, 2015 (the “Indenture”), between the Company and Wells Fargo Bank, National Association, as trustee (the “Trustee”), governing the Company’s new 5.00% Convertible Exchange Senior Notes due 2018 (the “New Notes”). $85 million in aggregate principal amount of the Company’s 5.00% Convertible Senior Notes due 2017 (the “Exchanged Notes”) were exchanged for $85 million in aggregate principal amount of New Notes in a private placement exempt from registration in reliance on Section 4(a)(2) of the Securities Act of 1933, as amended (the “Securities Act”).

This Current Report on Form 8-K does not constitute an offer to sell or the solicitation of an offer to buy any securities, nor shall it constitute an offer to sell, solicitation or sale in any jurisdiction in which such offer, solicitation or sale would be unlawful. These securities have not been registered under the Securities Act or any state securities laws and, unless so registered, may not be offered or sold in the United States or to U.S. persons except pursuant to an exemption from, or in a transaction not subject to, the registration requirements of the Securities Act and applicable state laws.

Descriptions of the New Notes and the Indenture are set forth in Item 8.01 in the Current Report on Form 8-K filed by the Company on June 4, 2015 and are incorporated by reference herein. Such descriptions and the descriptions otherwise herein do not purport to be complete and are qualified in their entirety by reference to the Indenture and the form of New Note, which are attached hereto as Exhibit 4.1 and incorporated by reference herein.

The information set forth above in Item 1.01 of this Current Report on Form 8-K is incorporated herein by reference.

The information set forth above in Item 1.01 of this Current Report on Form 8-K is incorporated herein by reference.

SIGNATURE

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.

EXHIBIT INDEX