UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q/A

(Amendment No. 2 to Form 10-Q)

(Mark One)

For the quarterly period ended June 30, 2015

or

For the transition period from                      to                     

Commission File Number: 001-33827

BG MEDICINE, INC.

(Exact name of registrant as specified in its charter)

(781) 890-1199

(Registrant’s telephone number, including area code)

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  x    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 (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  x    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.

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

As of July 31, 2015, the registrant had 8,742,638 shares of common stock outstanding.

EXPLANATORY NOTE

This Amendment No. 2 to the Quarterly Report on Form 10-Q/A (this “Amendment”) amends the Quarterly Report on Form 10-Q for the quarter ended June 30, 2015 filed by BG Medicine, Inc. with the Securities and Exchange Commission (the “Commission”) on August 14, 2015, as amended by Amendment No. 1 to the Quarterly Report on Form 10-Q filed on August 17, 2015 (collectively, the “Amended Report”). This Amendment is being filed solely for the purpose of furnishing the Interactive Data File as Exhibit 101, in accordance with Rule 405 of Regulation S-T, to Item 6 of Part II of the Amended Report.

Except as described above, no other changes have been made to the Amended Report and this Amendment does not modify or update disclosures in the Amended Report and does not reflect subsequent events occurring after date of the Amended Report. Accordingly, this Amendment should be read in conjunction with the Amended Report, which continues to speak as of the date of the Amended Report.

Item 6. EXHIBITS

(a)Exhibits

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.