SUPPLEMENTAL RETIREMENT AGREEMENT

Exhibit 10.1

SUPPLEMENTAL RETIREMENT AGREEMENT

This Supplemental Retirement Agreement (the “Agreement”) is entered into this 8th day of July, 2009 (the “Grant Date”) by and between Thermo Fisher Scientific Inc. (the “Company”) and Marijn Dekkers (the “Grantee”).

WHEREAS, the Grantee has served the Company as its Chief Executive Officer pursuant to the Employment Agreement;

WHEREAS, the Company desires to reward the Grantee for his past service to the Company and encourage and incentivize the Grantee to contribute to the long-term success of the Company;

NOW, THEREFORE, in consideration of the promises and mutual covenants contained herein and for other good and valuable  consideration, the receipt of which is mutually  acknowledged, the Company and the Grantee:

“Benchmark Index” means, with respect to any date, the average value of the S&P Industrials Composite Index for the 90 consecutive calendar days immediately preceding such date.  The value of the Benchmark Index on January 1, 2008 is $1,774.295.

“Cause” shall have the meaning set forth in the Employment Agreement.

“Change in Ownership or Control of the Company” is deemed to occur upon the consummation of a merger, consolidation, reorganization, recapitalization or statutory share exchange involving the Company or a sale or other disposition of all or substantially all of the assets of the Company in one or a series of transactions, provided that immediately following such event, the Stock is no longer publicly traded on an established securities market.

“Code” means the Internal Revenue Code of 1986, as amended.

“Committee” means the Compensation Committee of the Board of Directors of the Company or, in the absence of a Compensation Committee, the full Board of Directors.

“Disability” shall have the meaning set forth in the Employment Agreement.

“Employment Agreement” means the Amended and Restated Employment Agreement, effective as of April 7, 2008, by and between the Company and the Grantee.

“Final Performance-Based Phantom Shares” shall have the meaning set forth in Section 3(b)(ii).

“401(k) Excess Plan” means the non-qualified deferred compensation plan sponsored by the Company to provide a benefit that would have been provided in the Company’s Section 401(k) plan but for limitations imposed by Sections 402(g) and 401(a)(17) of the Code.

“Good Reason” shall have the meaning set forth in the Employment Agreement.

“Interest Rate” means the trailing 12-month average rate of return (interest only) of a ten-year Treasury Note.

“Mortality Table” means Table V under Treasury Regulations Section 1.72-9 (or such other table promulgated by the Internal Revenue Service that replaces this table).

“Payment Commencement Date” shall have the meaning set forth in Section 4.

“Performance-Based Phantom Shares” shall have the meaning set forth in Section 3.

“Phantom Share” means the right to receive the value of one share of Stock in accordance with the terms of this Agreement.

“Phantom Share Value” means (a) (i) the Stock Price as of the Separation from Service Date, (ii) multiplied by the number of vested Phantom Shares determined in accordance with Section 3, hereof, less (b) the value of the account balance of the Grantee under the 401(k) Excess Plan that is attributable to (x) Company contributions plus (y) an amount equal to investment gains (or losses) attributable to such Company contributions, calculated as if such contributions had been invested in the T. Rowe Price Retirement 2015 Fund (or such other balanced index fund that replaces this fund) offered by the Company as a measurement fund under the 401(k) Excess Plan.  For the avoidance of doubt, this offset does not take into account any amount attributable to elective deferred compensation by the Grantee under the 401(k) Excess Plan and any investment gains (or losses) thereon.

“Separation from Service” means the Grantee’s “separation from service” from the Company within the meaning set forth in Section 409A of the Code, determined in accordance with the presumptions set forth in Treasury Regulation Section 1.409A-1(h).

“Separation from Service Date” means the date the Grantee incurs a Separation from Service.

“Stock” means the common stock of the Company.

“Stock Price” means, with respect to a given date, the average closing price of the Stock for the 90 consecutive calendar days immediately preceding such date; provided, however, that, in the event of a Change in Ownership or Control of the Company, the Stock Price shall be the last reported closing price of the Stock on the immediately preceding full trading day immediately prior to the Change in Ownership or Control of the Company.

“Target Performance-Based Phantom Shares” shall have the meaning set forth in Section 3(b)(ii).

“Time-Based Phantom Shares” shall have the meaning set forth in Section 3.

“Total Shareholder Return” means the total return to a shareholder per share of Stock, from Stock Price appreciation, determined by comparing the Stock Price as of January 1, 2008 with the Stock Price on the last day of the applicable period,  plus cumulative dividends (compounded) during such period.  The Stock Price on January 1, 2008 is $57.72.

The Grantee shall forfeit all Time-Based Phantom Shares that have not vested as of the Grantee’s Separation from Service Date.