In a clinical decision support system (CDSS), the outcome of the system is related to the user interface directly. A successful CDSS should offer an efficient user interface to clinicians in order to get the most proper consultation results. This study is to assess the impact of user interface to the usability of CDSS. Two different types of input user interfaces were integrated into a well-established CDSS, namely, keyword-based interface and menu-based interface. The operating time of each interface was assessed, and the efficiency of the interfaces, effectiveness of the systems, and enjoyment of the users were also evaluated for degree of usability.