As the health care industry changes rapidly, hospital managerial performance and quality of service are becoming more critical. Recent studies show that the concepts and frameworks of the US internal control systems have greatly influenced on the development of the Taiwan internal control systems. This research surveys 100 Bureau of National Health Insurance certified hospitals to evaluate the implementation of the internal control systems in Taiwan by utilizing the control codes of the Taiwan accounting system as well as the integral framework for internal control of the Committee of Sponsoring Organizations of the Treadway Commission (COSO). By applying the results of this study, hospital administrators can identify the strengths and weaknesses of their internal control systems and set up action plans regarding the cost-benefit analyses. Although most hospitals declare the strong demands for internal controls, less than 30% of hospitals have assigned specialists to supervise and improve the internal controls. The research reveals that current Taiwan hospitals do not place high priority on the internal control systems. In addition, the results of this analysis describe how internal control systems in hospitals are implemented and can offer practical information for hospital administrators. Furthermore, the data reveals to what extent hospital administers understand internal control systems and to what extent they pay attention to the internal control systems. Finally, substantive suggestions have been proposed for government and related administrations of hospital institutions to establish or revise the internal control systems in order to be better confront with the drastically changing health care environment.