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Background: The planners and managers in health policy sector are responsible for policy making and planning of the health structure of a country. Therefore, they need to have access to reasonable and accurate information. Knowledge of managers about the applications of hospital information system is therefore of high importance. This study aimed to survey the knowledge of managers of Hamadan University of Medical Sciences (Iran) about the applications of hospital information system.Methods: This descriptive, analytical, cross-sectional study was performed on 40 managers of healthcare centers of Hamadan University of Medical Sciences during 2011. Data was collected by questionnaires. Descriptive statistics, central indices, and statistical dispersion were used for describing data. Kruskal-Wallis test was also used to analyze the data with SPSS.Findings: While the majority of the managers (77.5%) had moderate level of knowledge, 12.5% had desirable level of knowledge about managerial applications of hospital information system. Pharmacy managers had the greatest and radiology managers had the lowest levels of knowledge.Conclusion: Educational courses are necessary for better application of hospital information system in all parts of hospitals.