REORGANIZATION AGREEMENT

Exhibit 10.1

Execution Copy

REORGANIZATION AGREEMENT

Dated as of August 4, 2009

TABLE OF CONTENTS

REORGANIZATION AGREEMENT

          REORGANIZATION AGREEMENT, dated as of August 4, 2009, by and among Emdeon Inc., a Delaware corporation (the “ Company ”), EBS Acquisition II, LLC, a Delaware limited liability company (“ EBS Acquisition II ”), Hellman & Friedman Capital Associates VI, L.P., a Delaware limited partnership (“ H&F Capital Associates ”), Hellman & Friedman Capital Executives VI, L.P., a Delaware limited partnership (“ H&F Capital Executives ”), HFCP VI Domestic AIV, L.P., a Delaware limited partnership (“ HFCP Domestic ”), H&F Harrington AIV I, L.P., a Delaware limited partnership (“ Harrington LP ”), Hellman & Friedman Investors VI, L.P., a Delaware limited partnership (“ H&F GP ”), H&F Harrington Inc., a Delaware corporation (“ Harrington Inc. ”), H&F Harrington AIV II, L.P., a Delaware limited partnership (“ Harrington AIV ”), the ERX Members of EBS Master LLC set forth on Schedule IV hereto (the “ ERX Members ”), EBS Holdco I, LLC, a Delaware limited liability company (“ Sub 1 ”), EBS Holdco II, LLC, a Delaware limited liability company (“ Sub 2 ”), EBS Executive Incentive Plan LLC, a Delaware limited liability company (the “ Plan Member ”), and EBS Master LLC, a Delaware limited liability company (“ EBS Master ”).

RECITALS

          WHEREAS, the Board of Directors of the Company (the “ Board ”) has determined to effect an underwritten initial public offering (the “ IPO ”) of the Company’s Class A Common Stock, par value $0.00001 per share;

          WHEREAS, the Company, the Pre-Reorganization HF Members (as defined below), the ERX Members and EBS Acquisition II collectively own 100% of the outstanding equity interests in EBS Master (without giving effect to the Grant Units (as defined below) held by the Plan Member);

          WHEREAS, the Board, the Pre-Reorganization HF Members, the ERX Members and EBS Acquisition II have each determined that it is advisable and in the best interests of EBS Master and its equityholders to effect the Reorganization Transactions (as defined below) and the IPO; and

          WHEREAS, in connection with the consummation of the Reorganization Transactions and the IPO, the applicable parties hereto intend to enter into the Reorganization Documents (as defined below).

          NOW, THEREFORE, in consideration of the foregoing recitals and of the mutual promises hereinafter set forth, the parties hereto hereby agree as follows:

ARTICLE I

DEFINITIONS

          1.1 Certain Defined Terms . As used herein, the following terms shall have the following meanings:

          “ Additional IPO Closing ” means any additional closing of the sale of Class A Common Stock in the IPO pursuant to the exercise of the underwriters’ over-allotment option, which closing may occur on the same date and time as the IPO Closing.

          “ Amended and Restated Certificate of Incorporation ” has the meaning set forth in Section 2.1(a)(i).

          “ Board ” has the meaning set forth in the recitals of this Agreement.

          “ Class A Common Stock ” shall mean Class A Common Stock, par value $0.00001 per share, of the Company, having the rights set forth in the Amended and Restated Certificate of Incorporation.

          “ Class B Common Stock ” shall mean Class B Common Stock, par value $0.00001 per share, of the Company, having the rights set forth in the Amended and Restated Certificate of Incorporation.

          “ Common Stock ” means, collectively, the Class A Common Stock and Class B Common Stock.

          “ Company ” has the meaning set forth in the preamble of this Agreement.

          “ EBS Acquisition II ” has the meaning set forth in the preamble to this Agreement.

          “ EBS Acquisition Merger Agreement ” has the meaning set forth in Section 2.1(a)(iv).

          “ EBS Executive Equity Incentive Plan ” means the Amended and Restated EBS Executive Equity Incentive Plan of EBS Master.

          “ EBS Incentive Plan ” means the Amended and Restated EBS Incentive Plan of EBS Master.

          “ EBS Master ” has the meaning set forth in the preamble to this Agreement.

          “ EBS Master Management Incentive Plans ” means the EBS Executive Equity Incentive Plan and the EBS Incentive Plan.

          “ EBS Units ” has the meaning set forth in Section 2.1(a)(vii).

          “ ERX Class B Shares ” has the meaning set forth in Section 2.1(a)(ix).

          “ ERX Members ” has the meaning set forth in the preamble to this Agreement.

          “ GA EBS II Equityholders ” means, collectively, General Atlantic Partners 84, L.P., a Delaware limited partnership, GAP-W, LLC, GapStar, LLC, GAPCO GmbH & Co. KG, GAP Coinvestments CDA, L.P., GAP Coinvestments III, LLC, and GAP Coinvestments IV, LLC.

          “ GA Parties ” means, collectively, the GA EBS II Equityholders and General Atlantic Partners 83, L.P., a Delaware limited partnership (“ GAP 83 ”).

          “ Grant Units ” shall mean, collectively, the Grant A Units and Grant B Units of EBS Master that have been issued directly to the Plan Member on or prior to the date hereof.

          “ H&F Capital Associates ” has the meaning set forth in the preamble to this Agreement.

          “ H&F Capital Executives ” has the meaning set forth in the preamble to this Agreement.

          “ H&F Class B Shares ” has the meaning set forth in Section 2.1(a)(vii).

          “ H&F GP ” has the meaning set forth in the preamble to this Agreement.

          “ H&F Subscribing Party ” has the meaning set forth in Section 2.1(a)(vii).

          “ Harrington AIV ” has the meaning set forth in the preamble to this Agreement.

          “ Harrington Inc. ” has the meaning set forth in the preamble to this Agreement.

          “ Harrington LP ” has the meaning set forth in the preamble to this Agreement.

          “ Harrington Merger Agreement ” has the meaning set forth in Section 2.1(a)(vi).

          “ HFCP Domestic ” has the meaning set forth in the preamble to this Agreement.

          “ Investors Tax Receivable Agreement (Reorganizations) ” has the meaning set forth in Section 2.1(b)(i).

          “ Investors Tax Receivable Agreement (Exchanges) ” has the meaning set forth in Section 2.1(b)(i).

          “ Investors Tax Receivable Agreements ” means the Investors Tax Receivable Agreement (Reorganizations) and the Investors Tax Receivable Agreement (Exchanges).

          “ IPO ” has the meaning set forth in the recitals of this Agreement.

          “ IPO Closing ” means the initial closing of the sale of the Class A Common Stock in the IPO (without giving effect to any exercise of the underwriters’ over-allotment option).

          “ IPO Effective Time ” means the date and time on which the Registration Statement is declared effective by the Securities and Exchange Commission.

          “ Issued Shares ” has the meaning set forth in Section 3.2(d).

          “ Management Members ” means those individuals that are participants in the EBS Executive Equity Incentive Plan and listed on Schedule I hereto.

          “ Management Tax Receivable Agreement ” has the meaning set forth in Section 2.1(b)(ii).

          “ Person ” means any individual, corporation, limited liability company, limited or general partnership, joint venture, association, trust, unincorporated organization, government or any agency or political subdivision thereof, or any group comprised of two or more of the foregoing.

          “ Phantom Awards ” means awards issued under the EBS Incentive Plan.

          “ Plan Member ” has the meaning set forth in the preamble to this Agreement.

          “ Post-IPO HF Stockholders ” means, collectively, H&F Capital Associates, H&F Capital Executives, HFCP Domestic Harrington AIV and H&F GP.

          “ Post-Reorganization EBS Master Members ” means the Company, Sub 1, Sub 2, the H&F Subscribing Parties, the ERX Members and the Management Members.

          “ Pre-Reorganization HF Members ” means, collectively, H&F Capital Associates, H&F Capital Executives, HFCP Domestic and Harrington L.P.

          “ Registration Statement ” means the registration statement on Form S-1 (File No. 333-153451) filed by the Company with the Securities and Exchange Commission in connection with the IPO.

          “ Reorganization Documents ” means the documents listed on Schedule II hereto, each in the form attached as an exhibit hereto.

          “ Reorganization Transactions ” has the meaning set forth in Section 2.1.

          “ Restricted Stock Units ” means restricted stock units, issued under the Emdeon Inc. 2009 Equity Incentive Plan, entitling the holder to receive shares of Class A Common Stock upon vesting.

          “ Securities Act ” means the Securities Act of 1933, as amended.

          “ Sub 1 ” has the meaning set forth in the preamble to this Agreement.

          “ Sub 2 ” has the meaning set forth in the preamble to this Agreement.

          1.2 Other Definitional Provisions .

               (a) The words “hereof,” “herein” and “hereunder” and words of similar import when used in this Agreement shall refer to this Agreement as a whole and not to any particular provision of this Agreement, and Article and Section references are to this Agreement unless otherwise specified.

               (b) The meanings given to terms defined herein shall be equally applicable to both the singular and plural forms of such terms.

ARTICLE II

THE REORGANIZATION

          2.1 Transactions . Subject to the terms and conditions hereinafter set forth, and on the basis of and in reliance upon the representations, warranties, covenants and agreements set forth herein, the parties hereto shall take the actions described in this Section 2.1 (collectively, the “ Reorganization Transactions ”):

               (a) At such time prior to the IPO Effective Time as H&F GP and the GA Parties shall mutually agree, the applicable parties hereto shall take the actions set forth below (or cause such actions to take place):

          (i) The Company shall adopt and file with the Secretary of State of the State of Delaware an amended and restated certificate of incorporation of the Company, in the form of Exhibit A hereto (the “ Amended and Restated Certificate of Incorporation ”), that, among other things, shall (x) authorize the Company to issue up to 400,000,000 shares of Class A Common Stock and 52,000,000 shares of Class B Common Stock and (y) reclassify the outstanding shares of common stock held by the Company’s stockholders immediately prior to the filing of the Amended and Restated Certificate of Incorporation with the Secretary of State of the State of Delaware into an aggregate of

56,000,000 shares of Class A Common Stock, with each such stockholder receiving the number of shares of Class A Common Stock set forth opposite its name on Schedule V hereto.

          (ii) The Board shall adopt amended and restated bylaws of the Company in the form of Exhibit B hereto.

          (iii) The Company shall redeem from its existing stockholders an aggregate of 4,000,000 shares of Class A Common Stock in exchange for the rights to receive payments in respect of certain cash tax savings of the Company that are the subject of the Investors Tax Receivable Agreement (Reorganizations) and that relate to the Company and transactions entered into by the existing stockholders of the Company, which rights shall be immediately contributed by such stockholders to GA ITR Holdco, L.P., a Delaware limited partnership, in exchange for ownership interests in GA ITR Holdco, L.P. pursuant to Section 2.1(a)(xiii).

          (iv) Pursuant to the terms of an agreement and plan of merger to be entered into by and among the Company, EBS Acquisition II and Sub 1 in the form of Exhibit C hereto (the “ EBS Acquisition Merger Agreement ”), EBS Acquisition II shall merge with and into Sub 1, with Sub 1 being the surviving entity in the merger. In accordance with the terms of the EBS Acquisition Merger Agreement, as consideration for their interests in EBS Acquisition II, the GA EBS II Equityholders shall receive (x) an aggregate of 13,773,913 shares of Class A Common Stock and (y) the rights to receive payments in respect of certain cash tax savings of the Company that are the subject of the Investors Tax Receivable Agreement (Reorganizations) and that relate to EBS Acquisition II and transactions entered into by the GA EBS II Equityholders, which rights shall be immediately contributed by the GA EBS II Equityholders to GA ITR Holdco, L.P. in exchange for ownership interests in the GA ITR Holdco, L.P. pursuant to Section 2.1(a)(xiii).

          (v) Pursuant to a plan of liquidation, Harrington LP shall dissolve and distribute 1.064% of its interest in EBS Master to H&F GP and 98.936% of its interest in EBS Master to Harrington Inc.

          (vi) Pursuant to the terms of an agreement and plan of merger to be entered into by and among the Company, Harrington Inc. and Sub 2 in the form of Exhibit D hereto (the “ Harrington Merger Agreement ”), Harrington Inc. shall merge with and into Sub 2, with Sub 2 being the surviving entity in the merger. In accordance with the terms of the Harrington Merger Agreement, (x) as consideration for its interests in Harrington Inc, Harrington AIV, in its capacity as the sole stockholder of Harrington Inc., shall receive (x) 11,639,697 shares of Class A Common Stock and (y) the rights to receive payments in respect of certain cash tax

savings of the Company that are the subject of the Investors Tax Receivable Agreement (Reorganizations) and that relate to Harrington Inc. and transactions entered into by Harrington AIV, which rights shall be immediately contributed by Harrington AIV to H&F ITR Holdco, L.P., a Delaware limited partnership, in exchange for ownership interests in H&F ITR Holdco, L.P. pursuant to Section 2.1(a)(xiii).

          (vii) H&F Capital Associates, H&F Capital Executives, HFCP Domestic and H&F GP (each, an “ H&F Subscribing Party ”) each hereby subscribes for and each H&F Subscribing Party agrees to pay for, at a price of $0.00001 per share, that number of shares of Class B Common Stock (the “ H&F Class B Shares ”), equal to the number of units of EBS Master (“ EBS Units ”) owned by such H&F Subscribing Party immediately prior to the IPO Effective Time as set forth on Schedule III hereto. The H&F Subscribing Parties shall receive, along with the Class B Shares, the rights to enter into the Investors Tax Receivable Agreement (Exchanges), which rights shall be immediately contributed by the H&F Subscribing Parties to H&F ITR Holdco, L.P. pursuant to Section 2.1(a)(xiii).

          (viii) The Company shall issue the H&F Class B Shares to the H&F Subscribing Parties upon payment therefor.

          (ix) Each ERX Member hereby subscribes for and each ERX Member agrees to pay for, at a price of $0.00001 per share, that number of shares of Class B Common Stock (the “ ERX Class B Shares ”) equal to the number of EBS Units owned by such ERX Member immediately prior to the IPO Effective Time, as set forth on Schedule IV hereto.

          (x) The Company shall issue the ERX Class B Shares to the ERX Members upon payment therefor.

          (xi) The Company, EBS Master, Sub 1, Sub 2 and the H&F Subscribing Parties shall, and each agrees to, enter into Amendment No. 1 to the Fifth Amended and Restated Limited Liability Company Agreement of EBS Master, in the form of Exhibit E hereto, pursuant to which (x) Exhibit A to such limited liability company agreement shall be amended to reflect the addition of Sub 1, Sub 2 and H&F GP as members of EBS Master and (y) the Company shall be appointed as the sole managing member of EBS Master.

          (xii) The Company, the GA Parties, the Post-IPO HF Stockholders, the ERX Members and the Management Members shall enter into a stockholders agreement, in the form of Exhibit F hereto.

          (xiii) The existing stockholders of the Company and the GA EBS II Equityholders shall contribute all of their present and future rights in respect of the Investors Tax Receivable Agreement (Reorganizations) to GA ITR Holdco, L.P. in exchange for ownership interests in GA ITR Holdco, L.P., and Harrington AIV and the H&F Subscribing Parties shall contribute all of their present and future rights in respect of the Investors Tax Receivable Agreements to H&F ITR Holdco, L.P. in exchange for ownership interests in H&F ITR Holdco, L.P.

          (xiv) GA ITR Holdco, L.P. and H&F ITR Holdco, L.P. shall contribute all of their rights in respect of the Investors Tax Receivable Agreements to GA-H&F ITR Holdco, L.P., a Delaware limited partnership, in exchange for ownership interests in GA-H&F ITR Holdco, L.P.

          (xv) The Company shall provide the ERX Members and the Management Members at least 3 days’ notice prior to the closing of the transactions contemplated by this Section 2.1(a). Such notice may be given by email, telephone or telecopy, and shall be deemed immediately effective when given.

               (b) Prior to the IPO Closing, the applicable parties hereto shall take the actions set forth below (or cause such actions to take place):

          (i) The Company, GA-H&F ITR Holdco, L.P., H&F ITR Holdco, L.P. and GA ITR Holdco, L.P., shall enter into (A) the tax receivable agreement (the “ Investors Tax Receivable Agreement (Reorganizations) ”), in the form of Exhibit G hereto and (2) the tax receivable agreement (the “ Investors Tax Receivable Agreement (Exchanges) ”) in the form of Exhibit H hereto.

          (ii) The Company and the Management Members shall enter into a tax receivable agreement (the “ Management Tax Receivable Agreement ”), in the form of Exhibit I hereto.

               (c) With respect to the EBS Master Management Incentive Plans, after the IPO Effective Time and prior to the IPO Closing, the applicable parties hereto shall take the actions set forth below (or cause such actions to take place):

          (i) The Company, EBS Master, Sub 1, Sub 2 and the H&F Subscribing Parties shall, and each agrees to, enter into Amendment No. 2 to the Fifth Amended and Restated Limited Liability Company Agreement of EBS Master, in the form of Exhibit J hereto, pursuant to which all outstanding Grant Units issued to the Plan Member under the EBS Executive Equity Incentive Plan shall be converted into vested and

unvested EBS Units and certain other rights, including rights to enter into the Management Tax Receivable Agreement (the “ TRA Rights ”).

          (ii) The Company, as managing member of EBS Master shall adopt resolutions pursuant to which (x) the accumulated appreciation in value since the date of grant of all outstanding Grant Units issued to the Plan Member under the EBS Executive Equity Incentive Plan shall be converted into vested and unvested EBS Units (based on the public offering price of the Class A Common Stock in the IPO) and certain other rights, including the TRA Rights, (y) the Grant Units issued to the Plan Member under the EBS Executive Equity Incentive Plan shall be cancelled and (z) a plan of liquidation for the Plan Member shall be approved pursuant to which the EBS Units and TRA Rights shall be distributed to the members of the Plan Member and the class units issued by the Plan Member to the Management Members shall be cancelled.

          (iii) The Board of Directors of the Company (both for itself and as managing member of EBS Master) shall adopt resolutions pursuant to which (x) the accumulated appreciation in value since the date of grant of each