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 annual report on Form 10-KSB of MetaMorphix, Inc.
(the Registrant) for the year ended December 31, 2005 (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:

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| | 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):

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| | 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

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