The HIV/AIDS surveillance system in Japan, which began collecting data on the number of AIDS patients in 1984 and the number of HIV-infected persons in 1987, has played an important role in monitoring the trend and magnitude of Japan's HIV/AIDS epidemic and its distribution across various population subgroups. However, the system lacks any personal identifiers, making it impossible to eliminate duplication or to track cases for disease progression. It also does not permit the identification of the residence of HIV-infected persons because the residence of only the reporting physician is documented under the New Infectious Diseases Control Law, effective since April 1, 1999. The number of people with HIV/AIDS in Japan continues to grow. Among youth, sexually transmitted diseases, induced abortion, and sexual activities have shown a marked increase since the mid-1990s. Behavioral risk of infection for both injection drug users (IDUs) and men who have sex with men (MSM) remains alarmingly high. Accurate monitoring of infection rates is critical to the planning and evaluation of treatment, care and prevention programs. Japan should restructure its HIV/AIDS surveillance system to more accurately monitor the HIV/AIDS epidemic and related risk behaviors.