Exhibit 31.1**CERTIFICATION**I, Matthew P. Clifton, Chairman of the Board and Chief Executive Officer of Holly LogisticServices, L.L.C., the general partner of HEP Logistics Holdings, L.P., the general partner of HollyEnergy Partners, L.P., certify that:1. I have reviewed this quarterly report on Form 10-Q of Holly Energy Partners, L.P;2. Based on my knowledge, this quarterly report does not contain any untrue statement of amaterial fact or omit to state a material fact necessary to make the statements made, inlight of the circumstances under which such statements were made, not misleading withrespect to the period covered by this quarterly report;3. Based on my knowledge, the financial statements, and other financial information includedin 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 presentedin this quarterly report;4. The registrant’s other certifying officers and I are responsible for establishing andmaintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e)and 15d-15(e)) for the registrant and we have:a) designed such disclosure controls and procedures, or caused such disclosurecontrols and procedures to be designed under our supervision, to ensure thatmaterial information relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this quarterly report is being prepared;b) designed such internal control over financial reporting, or caused such internalcontrol over financial reporting to be designed under our supervision, to providereasonable assurance regarding the reliability of financial reporting and thepreparation of financial statements for external purposes in accordance withgenerally accepted accounting principles;c) evaluated the effectiveness of the registrant’s disclosure controls andprocedures and presented in this quarterly report our conclusions about theeffectiveness of the disclosure controls and procedures, as of the end of the periodcovered by this quarterly report based on such evaluation; andd) disclosed in this report any change in the registrant’s internal control overfinancial reporting that occurred during the period covered by this quarterly reporton Form 10-Q that has materially affected, or is reasonably likely to materiallyaffect, the registrant’s internal control over financial reporting; and5. The registrant’s other certifying officers and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’s auditors andthe audit committee of registrant’s board of directors (or persons performing the equivalentfunction):a) all significant deficiencies and material weaknesses in the design or operationof internal control over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize and reportfinancial information; andb) any fraud, whether or not material, that involves management or other employeeswho have a significant role in the registrant’s internal control over financialreporting.          Date: July 28, 2006 /s/ Matthew P. Clifton         Matthew P. Clifton    Chairman of the Board and Chief Executive Officer  
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