EXHIBIT 31.1

CERTIFICATIONS OF PRINCIPAL EXECUTIVE OFFICER
Pursuant to
Section 302 of the Sarbanes-Oxley Act of 2002

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|I,
  Edwin C. Quattlebaum, Ph.D., Chief Executive Officer, President and Co-Chairman
  of the Board of Directors of MetaMorphix, Inc., certify that:                                                                                                                                                                 
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|1.
  I have reviewed this annual report on Form 10-KSB of MetaMorphix, Inc. (the Registrant)
  for the year ended December 31, 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;
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|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;                   
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|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.
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|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                                                       
| |     |                                                                                    
| |     | Edwin
  C. Quattlebaum, Ph.D.                                                      
| |     | Chief Executive
  Officer, President and Co-Chairman of the Board of
  Directors of
| |     | MetaMorphix,
  Inc.                                                                

Date: June 8, 2007

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