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/A (Amendment No. 2) 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;

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;     
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| | 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                                                                                                    
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| | 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.                                                                                                 

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| | 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: February 29, 2008

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