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Objectives: To determine the prevalence and incidence of hepatitis A (HAV) and B (HBV) infection and vaccination in HIV-negative homosexual men in Sydney, and associated risk factors. Methods: An open prospective cohort study was conducted among a community-based sample of HIV-negative homosexual men in Sydney in 2001-02. Participants underwent a face-to-face interview, regarding demographics, sexual behavioural risk factors and sexually transmitted infections, and blood samples were collected. They were followed annually. Results: Nine hundred and three men completed a baseline interview by the end of 2002. Among them, 68% were seropositive to hepatitis A. The seroprevalence of prior hepatitis B infection was 19%, and 53% had serological evidence of HBV vaccination. Younger men were much more likely to be seronegative, with 48% and 46% of <25-year-olds being seronegative to HAV and HBV respectively. In multivariate analysis HAV and HBV infection were associated with increasing age, greater number of lifetime sex partners and HBV infection was also associated with previous sexually transmitted infections. HAV vaccination was associated with increasing age, greater number of lifetime sex partners, overseas travel in the last year and self-reported anogenital warts. HBV vaccination was associated with higher occupational status, greater lifetime number of sex partners and previous sexually transmitted infections. Conclusion: Substantial proportions of gay community attached young homosexual men are still at risk of HAV and HBV infection. This study points to a need for vaccination strategies which ensure high levels of hepatitis A and B immunity in young sexually active gay men.