**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. |