The main purpose of this study was to investigate the perceptions of the electromagnetic interference (EMI) caused by radio frequency identification (RFID) with medical devices among hospitals as well as to call the attention of medical institutions to the development of RFID applications. A survey sponsored by the Department of Health of Taiwan was conducted and the target subjects were every hospital in Taiwan (486 in total). The survey topics included testing of RFID interference with medical devices and perceptions of safety issues of RFID. The main targets of the survey were the Chief Information Officers (CIOs) or the main person responsible for RFID systems in each hospital. Of the original 486 questionnaires mailed, 273 were returned. A return rate of 56.17% was obtained. The survey results revealed that only six hospitals had carried out tests on interference by RFID with medical devices, and the results of these tests indicated that RFID does not interfere with medical devices. A majority of hospitals understood that RFID may interfere with medical devices but did not think that this would seriously harm patients. The application of RFID in the healthcare industry is certainly promising; however, EMI issues must be appropriately handled. This study asserts that most hospitals do not understand or pay insufficient attention to the issue of RFID interference with patient safety or medical devices. In addition, most hospitals believe that the problem of RFID should be resolved by RFID vendors. Therefore, this study argues that medical institutions should develop more understanding of RFID issues and that more attention should be given to the potential problems of RFID interference when developing RFID applications.