Background Hepatitis A outbreaks are well documented among men who have sex with men (MSM). This analysis examines characteristics associated with hepatitis A virus (HAV) infection among a large group of young adult MSM from five USA cities. Methods: The Young Men’s Survey was a cross-sectional prevalence study of HIV infection and related behavioural risk factors among MSM aged 15–29 years during 1994–2000. Serum specimens from HIV-negative participants were retrospectively tested for antibodies to HAV (anti-HAV). Data were stratified by ethnicity and analysed with logistic regression. Results: Overall anti-HAV prevalence was 18.4% among the 2708 participants, and varied by ethnicity from 6.9 to 45.3% and was highest among Hispanic and Asian men (P < 0.001). Prevalence increased with age across all racial/ethnic groups. Among white men, anti-HAV positivity was associated with having 20 or more lifetime male sex partners for those aged 15–22 years (adjusted odds ratio (AOR) = 2.1, 95% confidence interval (CI) = 1.0–4.1) and ever having had unprotected anal sex for those aged 23–29 years (AOR = 2.4, 95% CI = 1.2–4.5). Conclusions: Factors associated with a history of HAV infection among MSM in non-outbreak settings are probably similar to those among non-MSM. MSM are still at risk for HAV infection as a result of outbreaks occurring in MSM communities. Additional studies of hepatitis A vaccination coverage are needed to determine if strategies to vaccinate MSM are adequate.