**Exhibit 31.1**

**Certification Pursuant to Rule 13a-14(a), as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002**

| I, Randall L. Marcuson,   certify that: |
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|                                    | 1.     I   have reviewed this quarterly report on Form 10-Q of Embrex, Inc.; |
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|                                    | 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)) and internal control over financial   reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) 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) Designed such internal   control over financial reporting, or caused such internal control over   financial reporting to be designed under our supervision, to provide   reasonable assurance regarding the reliability of financial reporting and the   preparation of financial statements for external purposes in accordance with   generally accepted accounting principles; |
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|                                    |   | (c) 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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|                                    |   | (d) 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; and |
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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): |
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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 |
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|                                    |   | (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. |

Date: November 6, 2006

|   |   | /s/ Randall L. Marcuson                 |
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|   |   |                                         |
|   |   | Randall L. Marcuson                     |
|   |   | President and Chief Executive   Officer |

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