Background: This study investigated the prevalence of male homosexual behaviour among adult men and of HIV and AIDS among men who have sex with men (MSM) and non-MSM in Japan. Methods: An anonymous self-administered postal questionnaire, and national HIV and AIDS notifications. Results: Same-sex sexual experience was reported by 2.0% of respondents. The prevalence of HIV and AIDS was 0.8818% among MSM and 0.0130% among non-MSM, indicating that HIV and AIDS are 68 times more prevalent among MSM. Conclusion: Our findings underestimate homosexual and HIV prevalence due to several methodological limitations. The high prevalence of HIV and AIDS among MSM in comparison with non-MSM indicates the urgent need to prioritise funding and programs targeting MSM in Japan.