We conducted a questionnaire survey regarding the current activities for protecting patients' privacy and the security of information systems (IS) related to the clinical laboratory departments of university hospitals, certified training facilities for clinical laboratories, and general hospitals in Yamaguchi Prefecture. The response rate was 47% from 215 medical institutions, including three commercial clinical laboratory centers. The results showed that there were some differences in management activities among facilities with respect to continuing education, the documentation or regulation of operational management for paper records, electronic information, remaining samples, genetic testing, and laboratory information for secondary use. They were suggested to be caused by differences in functions between university and general hospitals, differences in the scale of hospitals, or whether or not hospitals have received accreditation or ISO 15189. Regarding the IS, although the majority of facilities had sufficiently employed the access control to IS, there was some room for improvement in the management of special cases such as VIPs and patients with HIV infection. Furthermore, there were issues regarding the login method for computers shared by multiple staff, the showing of the names of personnel in charge of reports, and the risks associated with direct connections to systems and the Internet and the use of portable media such as USB memory sticks. These results indicated that further efforts are necessary for each facility to continue self-assessment and make improvements.