EXHIBIT 31.1
                  CERTIFICATIONS OF PRINCIPAL EXECUTIVE OFFICER
                                   PURSUANT TO
                  SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

      I, Edwin C. Quattlebaum, Ph.D., Chief Executive Officer, President and
Co-Chairman of the Board of Directors of MetaMorphix, Inc., certify that:

      1. I have reviewed this quarterly report on Form 10-QSB of MetaMorphix,
Inc. (the "Registrant") for the period ended June 30, 2006 (the "Report");

      2. Based on my knowledge, this Report does not contain any untrue
statement of a material fact or omit to state a material fact necessary to make
the statements made, in light of the circumstances under which such statements
were made, not misleading with respect to the period covered by this Report;

      3. Based on my knowledge, the financial statements, and other financial
information included in this Report, fairly present in all material respects the
financial condition, results of operations and cash flows of the Registrant as
of, and for, the periods presented in this Report;

      4. The Registrant's other certifying officer and I are responsible for
establishing and maintaining disclosure controls and procedures (as defined in
Exchange Act Rules 13a-15(e) and 15d-15(e)) for the Registrant and have:

            a) designed such disclosure controls and procedures, or caused such
      disclosure controls and procedures to be designed under our supervision,
      to ensure that material information relating to the Registrant, including
      its consolidated subsidiaries, is made known to us by others within those
      entities, particularly during the period in which this Report is being
      prepared;

            b) evaluated the effectiveness of the Registrant's disclosure
      controls and procedures and presented in this Report our conclusions about
      the effectiveness of the disclosure controls and procedures, as of the end
      of the period covered by this Report based on such evaluation; and

            c) disclosed in this Report any change in the Registrant's internal
      control over financial reporting that occurred during the Registrant's
      most recent fiscal quarter (the Registrant's fourth fiscal quarter in the
      case of an annual report) that has materially affected, or is reasonably
      likely to materially affect, the Registrant's internal control over
      financial reporting.

      5. The Registrant's other certifying officer and I have disclosed, based
on our most recent evaluation of internal control over financial reporting, to
the Registrant's auditors and the audit committee of the Registrant's board of
directors (or persons performing the equivalent functions):

            a) all significant deficiencies and material weaknesses in the
      design or operation of internal control over financial reporting which are
      reasonably likely to adversely affect the Registrant's ability to record,
      process, summarize and report financial information; and

            b) any fraud, whether or not material, that involves management or
      other employees who have a significant role in the Registrant's internal
      control over financial reporting.

         By:                    /s/ Edwin C. Quattlebaum, Ph.D.


                                 Edwin C. Quattlebaum, Ph.D.
             CHIEF EXECUTIVE OFFICER, PRESIDENT AND CO-CHAIRMAN OF THE BOARD OF
                                        DIRECTORS OF
                                     METAMORPHIX, INC.

Date:  October 3, 2006