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As the IT operation in the other Enterprise, the implementation of IT in Higher Education has to be directed and aligned with organizational strategy and program. The strategic alignment is one of five IT Governance focus areas. This paper presents the results, discussions and recommendations of IT Governance in Higher Education self assessment which is performed by COBIT 4.1 framework. The assessment is performed to IT Governance implementation in Mercu Buana University as a case study. The study result shows that the implementation of IT Governance in the university is still in the first stage of its development. Based on these results and some evidences collected, the study proposes some improvements such: it is needed to provide IT master plan, data and process custodian settlements must be performed, and the setup of such organizational structure which has capabilities enough to coordinate and deal with process / data owner and key user to drive University's IT Governance. 