Exhibit 31.1**CERTIFICATION**I, Matthew P. Clifton, 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 report does not contain any untrue statement of a materialfact or omit to state a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading with respect to theperiod covered by this report;3. Based on my knowledge, the financial statements, and other financial information includedin this report, fairly present in all material respects the financial condition, results ofoperations and cash flows of the registrant as of, and for, the periods presented in thisreport;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)) and internal control over financial reporting (as defined in Exchange ActRules 13a-15(f) and 15d-15(f)) 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 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 report our conclusions about the effectiveness ofthe disclosure controls and procedures, as of the end of the period covered by thisreport 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 report on Form10-Q that has materially affected, or is reasonably likely to materially affect, theregistrant’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: November 2, 2007 /s/ Matthew P. Clifton   Matthew P. Clifton   Chairman of the Board and Chief Executive Officer   
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