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Objective: To examine HIV prevalence and its associated factors among men who have sex with men (MSM) and provide the evidence for the intervention program among MSM., Methods: A face-to-face questionnaire interview was conducted among MSM recruited by snowball sampling method in Yuzhong, Jiulongpo and Shapingba district of Chongqing from July to September, 2007. Totally, 1044 MSM were recruited. Associated factors with HIV prevalence were analyzed using forward stepwise logistic regression that HIV status was the dependent variable and demographics, AIDS awareness, sexual behaviors and the status of the intervention were independent variables., Results: A total of 1044 MSM were surveyed. The rate of AIDS awareness was 89.5% among MSM. The rate of unprotected anal sex during the past 6 months was 63.8%. The prevalence of HIV and syphilis was 8.5% (89/1044) and 12.5% (131/1044) respectively. The multivariate analysis identified that the older MSM (OR = 1.69, 95% CI: 1.13 - 2.52), junior school education (OR = 1.89, 95% CI: 1.17 - 3.05), younger than 18 years old of the first sex (OR = 3.11, 95% CI: 1.20 - 8.02), more than 10 sexual partners (OR = 2.24, 95% CI: 1.24 - 4.02), the history of having sex with women (OR = 2.40, 95% CI: 1.64 - 3.51) and syphilis infection (OR = 4.52, 95% CI: 2.77 - 7.38) were independent risk factors associated with HIV infection., Conclusion: The rate of unprotected anal sex was high, so were the prevalence of HIV and syphilis among MSM. It should be urgent to conduct the intervention to stop AIDS rapid transmission among MSM.