**EXHIBIT        31.1**

**CERTIFICATION**

**CERTIFICATION      OF THE CHIEF EXECUTIVE OFFICER**

**PURSUANT      TO**

**SECURITIES      EXCHANGE ACT FULES 13A-14 AND 15D-14**

**AS      ADOPTED PURSUANT TO SECTION 302**

**OF      THE SARBANES-OXLEY ACT OF 2002**

| 1. | I                have reviewed this quarterly report on Form 10-QSB of ThermoEnergy                Corporation; |
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| 2. | Based                on my knowledge, this quarterly 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 quarterly report; |
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| 3. | Based                on my knowledge, the financial statements, and other financial information                included in this quarterly 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 quarterly                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 small                business issuer and have: |
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| 5. | The                registrant’s other certifying officer and I have disclosed, based on my                most recent evaluation in internal control over financial reporting,                to                the registrant’s auditors and the audit committee of registrant’s board of                directors (or persons performing the equivalent                functions): |
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|---------------------------------------------------|----------------------------------------------------------------------|--------------|--------------|
| Date:              November 14,              2006 |                                                                 |
|                                              |                                                            |    |    |
| By:                                               |  /s/              Dennis              C. Cossey                 |         |         |
|                                              | Name:                Dennis C. CosseyTitle:                President |              |
|                                              |                                                                 |         |

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