BG MEDICINE, INC. THIRD AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

Exhibit 4.2

Execution Version

BG MEDICINE, INC.

THIRD AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

         THIS THIRD AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT (the " Agreement ") is made as of May 1, 2007, by and among BG Medicine, Inc ., a Delaware corporation (the " Company "), and the holders of capital stock of the Company as set forth on Schedule A hereto (the " Preferred Stockholders ").

RECITALS:

        A.    Whereas the Preferred Stockholders own certain shares of Series A Preferred Stock, par value $0.001 per share, of the Company (the " Series A Preferred Stock "), Series A-1 Preferred Stock, par value $0.001 per share, of the Company (the " Series A-l Preferred Stock "), Series B Preferred Stock, par value $0.001 per share, of the Company (the " Series B Preferred Stock ") and Series C Preferred Stock, par value $0.001 per share, of the Company (the " Series C Preferred Stock " and collectively with the Series A Preferred Stock, Series A-1 Preferred Stock and Series B Preferred Stock, the " Preferred Stock ") convertible into shares of Common Stock, par value $0.001 per share, of the Company (the " Common Stock ").

        B.    Whereas the Company, the Preferred Stockholders and certain other parties entered into an Investor Rights Agreement dated as of April 20, 2001, as amended (the " Investor Rights Agreement ").

        C.    Whereas the Company, the Preferred Stockholders and certain other parties amended and restated the Investor Rights Agreement on October 28, 2004, as amended (the " First Amended Agreement ").

        D.    Whereas the Company, the Preferred Stockholders and certain other parties are parties to a Second Amended and Restated Investor Rights Agreement dated as of March 28, 2005, as amended (the " Second Amended Agreement ").

        E.    Whereas the Company and the Preferred Stockholders holding at least 50% of the Registrable Securities (as defined in the Second Amended Agreement) desire to amend and re-state in its entirety the Second Amended Agreement by their execution of this Agreement.

        Now, therefor, the parties hereto agree as follows:

AGREEMENT:

        1.     Certain Definitions.     As used in this Agreement, the following terms shall have the following respective meanings:

        " Board " shall mean the Company's Board of Directors.

        " Commission " shall mean the U.S. Securities and Exchange Commission.

        " Exchange Act " shall mean the U.S. Securities Exchange Act of 1934, as amended, and the rules and regulations of the Commission promulgated thereunder, all as the same shall be in effect from time to time.

        " Holders " or " Holders of Registrable Securities " shall mean the Preferred Stockholders and any Person who shall have acquired Registrable Securities from the Preferred Stockholders as permitted

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herein, either individually or jointly, as the case may be, in a transaction pursuant to which registration rights are transferred pursuant to Section 10 hereof.

        " IPO " shall mean an initial public offering in which all outstanding shares of Preferred Stock are converted pursuant to the automatic conversion provisions contained in the Company's certificate of incorporation, as amended from time to time.

        " Person " shall mean an individual, a partnership, a corporation, a limited liability company, an association, a joint stock company, a trust, a joint venture, an unincorporated organization or a governmental or quasi-governmental entity, or any department, agency or political subdivision thereof or any other entity of any kind.

        " Registrable Securities " shall mean (i) any shares of Common Stock at any time beneficially owned by the Preferred Stockholders or their respective affiliates (including shares of Common Stock issued or issuable upon conversion or exercise of the Preferred Stock), as the case may be; and (ii) any shares of Common Stock issued or issuable in respect of the securities referred to in clause (i) above, whether to satisfy interest or dividend payments or upon any stock split, stock dividend, recapitalization or otherwise, until, in the case of any such security, it is (A) sold pursuant to an effective registration statement under the Securities Act; (B) eligible to be sold into the public market without regard to volume limitations under Rule 144(k) promulgated under the Securities Act (or any successor rule); (C) sold pursuant to Rule 144 under the Securities Act (or any successor rule); or (D) sold by a Person in a transaction in which registration rights are not transferred pursuant to Section 8 hereof. Whenever reference is made in this Agreement to a request or consent of holders of a certain number or percentage of Registrable Securities, the determination of such number or percentage shall be calculated on the basis of shares of Common Stock issued or issuable pursuant to the conversion of shares of Preferred Stock.

        The terms " register ," " registered " and " registration " refer to a registration effected by preparing, filing and having declared effective a registration statement in compliance with the Securities Act.

        " Registration Expenses " shall mean (i) all expenses, other than Selling Expenses (defined below), incurred by the Company in complying with Sections 2 or 3 hereof, including without limitation, all registration, qualification and filing fees, exchange or quotation medium listing fees, printing and delivery expenses, escrow and custodian fees, fees and disbursements of counsel for the Company, blue sky fees and expenses and the expenses of accountants for the Company including the expenses of any special audits incident to or required by any such registration and (ii) the reasonable fees and disbursements of one counsel chosen by the holders of a majority of the Registrable Securities included in such registration for the purpose of rendering a legal opinion on behalf of such holders in connection with any Demand Registration or Piggyback Registration.

        " Securities Act " shall mean the U.S. Securities Act of 1933, as amended, and the rules and regulations of the Commission promulgated thereunder, all as the same shall be in effect from time to time.

        " Selling Expenses " shall mean all underwriting discounts, selling commissions and stock transfer taxes and the costs, fees and expenses of any accountants, attorneys (other than the cost, fees and expenses of attorneys which are Registration Expenses) or other experts retained by the Holders.

        2.     Holders Demand Registrations.     

•         (a)     Request for Registration.     Any Holder or Holders who collectively hold Registrable Securities representing at least 40% of the Registrable Securities then outstanding shall have the right (subject to the limitations set forth below), exercisable by written notice to the Company (each a " Registration Request "), to have the Company prepare and file with the Commission a registration statement under the Securities Act covering the Registrable Securities that are the

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• subject of such request (each, a " Demand Registration "); provided, that the Company shall not be obligated to prepare and file a registration statement (A) within the first six months after the date of effectiveness of a registration statement filed under the Securities Act in respect of an initial public offering of shares of Common Stock of the Company unless the Registrable Securities that are the subject of such request have an expected aggregate offering price to the public of at least U.S.$3,000,000, or (B) if neither Form S-3 nor another short form registration statement is available to the Company to fulfill such Registration Request, unless the Registrable Securities that are the subject of such request have an expected aggregate offering price to the public of at least U.S.$1,000,000. Within 10 days after receipt of any such request, the Company will give written notice of such requested registration to all other Holders of Registrable Securities. The Company shall include such other Holders' Registrable Securities in such offering if they have responded affirmatively within 10 days after the receipt of the Company's notice. Subject to the foregoing, the Holders shall be permitted one Demand Registration hereunder.

          A request for registration under this Section 2(a) will not count as a Demand Registration until the registration statement has become effective and remained effective until the earlier of 30 days and the sale of all securities registered thereunder (unless such registration statement has not become effective due solely to the actions or failure to act with respect to such registration of the Holders requesting such registration, including a request by such Holders that such registration be withdrawn).

          (b)     Priority on Holders Demand Registrations.     If a Demand Registration is an underwritten offering and the managing underwriters advise the Company in writing that in their opinion the number of Registrable Securities and, if permitted hereunder, other securities requested to be included in such offering, exceeds the number of Registrable Securities and other securities, if any, which can be sold in such offering without adversely affecting the marketability of the offering, the Company will include in such registration:

  •             i.  first, the Registrable Securities requested to be included in such registration by the Holders (or, if necessary, such Registrable Securities pro rata among the Holders thereof based upon the number of Registrable Securities owned by each such Holder or such other arrangement agreed to among the Holders); and

               ii.  thereafter, other securities requested to be included in such registration, as determined by the Company.

          The Holders of any Registrable Securities to be included in such an underwritten offering shall enter into an underwriting agreement (which shall be in customary form, may include agreements as to indemnification and contribution and shall provide that the representations and warranties by the Company to and for the benefit of such underwriters, shall also be made to and for the benefit of such Holders).

          (c)     Restrictions on Demand Registration.     The Company may postpone or suspend, for up to 90 days in any 12-month period, the filing or the effectiveness of a registration statement for a Demand Registration if the Board determines in good faith and notifies the Holders in writing that such Demand Registration (i) would reasonably be expected to have a material adverse effect on (x) any proposal or plan by the Company to engage in any financing, acquisition or disposition of assets (other than in the ordinary course of business) or (y) any merger, consolidation, tender offer or similar transaction or (ii) would require disclosure of any information that the Board determines in good faith the disclosure of which would be detrimental to the Company, provided , however , that in such event, the Holders initially requesting such Demand Registration shall be entitled to withdraw such request and, if such request is withdrawn, such Demand Registration will not count as a permitted Demand Registration hereunder and the Company will pay any Registration Expenses in connection with such registration.

          (d)     Selection of Investment Bankers and Managers.     The Company will have the right to select the investment banker(s) and manager(s) to administer an offering pursuant to the Demand Registration, subject to the approval of the holders of a majority of the Registrable Securities, which will not be unreasonably withheld, delayed or conditioned.

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•         (e)   The Company represents and warrants that it is not a party to, or otherwise subject to, any agreement, other than this Agreement, granting registration rights to any other Person with respect to any securities of the Company.

        3.     Piggyback Registrations.     

•         (a)     Right to Piggyback.     If at any time after the Company has closed an IPO, the Company shall propose to register shares of Common Stock under the Securities Act (other than in a registration statement relating solely to sales of securities to participants in a Company dividend reinvestment plan, or Form S-4 or S-8 or any successor form or in connection with an acquisition or exchange offer or an offering of securities solely to the existing shareholders or employees of the Company), the Company (i) will give prompt written notice to all Holders of Registrable Securities of its intention to effect such a registration and (ii) subject to Section 2(b) and Section 3(b) and the other terms of this Agreement, will include in such registration all Registrable Securities which are permitted under applicable securities laws to be included in the form of registration statement selected by the Company and with respect to which the Company has received written requests for inclusion therein within 30 days after the receipt of the Company's notice (each, a " Piggyback Registration "); provided , however , that the Company shall not be obligated to include Registrable Securities of a Holder eligible for resale into the public market without regard to volume limitations under Rule 144(k) promulgated under the Securities Act. The Holders will be permitted to withdraw all or any part of the Registrable Securities from a Piggyback Registration at any time prior to the effective date of such Piggyback Registration.

          (b)     Priority on Piggyback Registrations.     If a Piggyback Registration is to be an underwritten offering, and the managing investment bank advises the Company in writing that in their opinion the number of securities requested to be included in such registration exceeds the number which can be sold in such offering without adversely affecting the marketability of the offering, the Company will include in such registration:

  •             i.  first, the securities the Company proposes to sell for its own account;

               ii.  second, the Registrable Securities requested to be included in such registration by the Holders and any securities requested to be included in such registration by any other Person pursuant to a demand registration request, other than Persons having a lower priority of registration than the Holders, pro rata among the Holders of such Registrable Securities and such other Persons, on the basis of the number of securities requested to be included in such registration by each of such Holders and such other Persons; and

              iii.  thereafter, other securities requested to be included in such registration, as determined by the Company.

          The Holders of any Registrable Securities to be included in an underwritten offering shall enter into an underwriting agreement (which shall be in customary form, may include agreements as to indemnification and contribution, and shall provide that the representations and warranties by the Company to and for the benefit of such underwriters, shall also be made to and for the benefit of such Holders). Notwithstanding (i) - (iii) above, the number of securities held by each Holder of Series B Preferred Stock to be included in such registration shall not be reduced to less than 20% of the total number of securities to be included in such registration.

          (c)     Right to Terminate Registration.     If at any time after giving written notice of its intention to register any of its securities as set forth in Section 3(a) and prior to the effective date of the registration statement filed in connection with such registration, the Company shall determine for any reason not to register such securities, the Company may, at its election, give written notice of such determination to each Holder of Registrable Securities and thereupon be relieved of its

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  obligation to register any Registrable Securities in connection with such registration (but not from its obligation to pay the Registration Expenses in connection therewith as provided herein).

          (d)     Selection of Underwriters/Placement Agents.     The Company will have the right to select the investment banker(s) and manager(s) to administer an offering pursuant to a Piggyback Registration, subject to the approval of the holders of a majority of the Registrable Securities, which approval will not be unreasonably withheld, delayed or conditioned.

        4.     Expenses of Registration.     Except as otherwise provided herein or as may otherwise be prohibited by applicable law, all Registration Expenses incurred in connection with all registrations pursuant to Sections 2 and 3 hereof shall be borne by the Company. All Selling Expenses relating to securities registered on behalf of the Holders of Registrable Securities shall be borne by such Holders.

        5.     Holdback Agreements.     

•         (a)   The Company agrees (i) if requested by the underwriters managing the offering, not to effect any public sale or distribution of its equity securities, or any securities convertible into or exchangeable or exercisable for such securities, during the 10-day period prior to, and during the 90-day period following, the effective date of any underwritten Demand Registration or any underwritten Piggyback Registration (except as part of such underwritten registration or pursuant to registration statements on Form S-4 or Form S-8 or any successor form), and (ii) to use its best efforts to cause its officers and directors and each holder of at least 5% (on a fully-diluted basis) of its outstanding shares of Common Stock, or any securities convertible into or exchangeable or exercisable for shares of Common Stock, purchased from the Company at any time after the date of this Agreement (other than in a registered public offering) to agree not to effect any public sale or distribution (including sales pursuant to Rule 144) of any such securities during such periods (except as part of such underwritten registration, if otherwise permitted), unless the underwriters managing the registered public offering otherwise agree.

          (b)   If requested by the managing underwriter(s) in an underwritten offering of Common Stock or securities convertible for Common Stock of the Company (including without limitation the Company's initial public offering of Common Stock), each Holder agrees, unless such Holder is a participant in such offering, not to effect any offer, sale, distribution or transfer, including a sale pursuant to Rule 144 (or any similar provision then effect) under the Securities Act (except as part of such underwritten registration), during the 10-day period prior to, and during the 180-day period in the case of the Company's initial public offering, if applicable, or the 90-day period in the case of any other public offering of Common Stock (or, in each case, such shorter period as may be agreed to in writing by the Company and the Holders of at least 50% of the Registrable Securities) following, the effective date of such Registration Statement; provided , however , that (i) no Holder shall be required to enter into more than two such agreements in any 12-month period and (ii) no Holder shall be required to enter into such an agreement unless all Persons entitled to registration rights who are not parties to this Agreement, all other Persons selling shares in such offering, all Persons holding in excess of 5% (on a fully diluted basis) of the Company's outstanding shares of Common Stock (other than that purchased in a registered public offering) and all executive officers and directors of the Company shall also have agreed not to offer, sell, distribute a transfer under the circumstances and pursuant to the terms set forth in this Section 5(b).

        6.     Registration Procedures.     Whenever the Holders of Registrable Securities have requested that any Registrable Securities be registered pursuant to this Agreement, the Company will use its best efforts to effect the registration and the sale of such Registrable Securities in accordance with the

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intended method or methods of distribution thereof, and pursuant thereto the Company will under the time frames provided herein, or if not so provided, as expeditiously as possible:

•         (a)   prepare and file with the Commission a registration statement on any appropriate form for which the Company qualifies with respect to such Registrable Securities and use its best efforts to cause such registration statement to become effective ( provided that before filing a registration statement or prospectus or any amendments or supplements thereto, the Company will (i) furnish to the counsel selected by the Holders copies of all such documents proposed to be filed, which documents will be subject to the review of such counsel, and (ii) notify each Holder of Registrable Securities covered by such registration of any stop order issued or threatened by the Commission);

          (b)   prepare and file with the Commission such amendments and supplements to such registration statement and the prospectus used in connection therewith as may be reasonably necessary to keep such registration statement effective for a period equal to the shorter of (i) 180 days and (ii) the time by which all securities covered by such registration statement have been sold, and comply with the provisions of the Securities Act with respect to the disposition of all securities covered by such registration statement during such period in accordance with the intended methods of disposition by the sellers thereof set forth in such registration statement;

          (c)   furnish to each seller of Registrable Securities such number of copies of such registration statement, each amendment and supplement thereto, the prospectus included in such registration statement (including each preliminary prospectus) and such other documents as such seller may reasonably request in order to facilitate the disposition of the Registrable Securities owned by such seller;

          (d)   use all reasonable efforts to register or qualify such Registrable Securities under the securities or blue sky laws of such jurisdictions as any seller reasonably requests and do any and all other acts and things which may be reasonably necessary or advisable to enable such seller to consummate the disposition in such jurisdictions of the Registrable Securities owned by such seller ( provided that the Company will not be required to (i) qualify generally to do business in any jurisdiction where it would not otherwise be required to qualify but for this Section 6(d), (ii) subject itself to taxation in any jurisdiction or (iii) take any action that would subject it to general service of process in any such jurisdiction);

          (e)   promptly notify each seller of such Registrable Securities, at any time when a prospectus relating thereto is required to be delivered under the Securities Act, of the happening of any event as a result of which the prospectus included in such registration statement contains an untrue statement of a material fact or omits any material fact nec