<Page> Exhibit 99.906.Cert FORM N-CSR ITEM 10(b) EXHIBIT CERTIFICATION PURSUANT TO 18 U.S.C. SECTION 1350, AS ADOPTED PURSUANT TO SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002 The undersigned hereby certify in their capacity as Treasurer and President, respectively, of EATON VANCE MUTUAL FUNDS TRUST (the "Trust") (on behalf of Eaton Vance Tax-Managed Mid-Cap Core Fund]), that: (a) the Annual Report of the Trust (on behalf of Eaton Vance Tax-Managed Mid-Cap Core Fund) on Form N-CSR for the period ended October 31, 2003 (the "Report") fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended; and (b) the information contained in the Report fairly presents, in all material respects, the financial condition and the results of operations of the Trust (on behalf of Eaton Vance Tax-Managed Mid-Cap Core Fund) for such period. A SIGNED ORIGINAL OF THIS WRITTEN STATEMENT REQUIRED BY SECTION 906 HAS BEEN PROVIDED TO THE TRUST AND WILL BE RETAINED BY THE TRUST AND FURNISHED TO THE SECURITIES AND EXCHANGE COMMISSION OR ITS STAFF UPON REQUEST. EATON VANCE MUTUAL FUNDS TRUST (On behalf of Eaton Vance Tax-Managed Mid-Cap Core Fund) Date: December 16, 2003 ----------------- /S/ James L. O'Connor - ----------------------- James L. O'Connor Treasurer Date: December 16, 2003 ----------------- /S/ Thomas E. Faust Jr. - ----------------------- Thomas E. Faust Jr. President