Background Many countries are facing concentrated HIV epidemics among vulnerable populations, including men who have sex with men (MSM). Unprotected anal intercourse (UAI) is the main HIV transmission route among them and its understanding in the different cultures and how it relates to HIV transmission, re-infection and development of HIV antiretroviral resistance has important public health implications. Data on UAI among Brazilian MSM are scarce. This study aims to evaluate the prevalence and associated factors of UAI among HIV-infected MSM who had sex with seronegative or male partners with an unknown serostatus. Method A cross-sectional study nested in a cohort was conducted in Rio de Janeiro, Brazil. The one hundred and fifty five MSM included in the study answered an ACASI interview and provided biological samples. Generalized linear models were used to identify variables associated with UAI. Results Overall, UAI with an HIV-negative or unknown serostatus male partner was reported by 40.6% (63/155) of MSM. Lifetime sexual abuse or domestic violence was reported by 35.9%, being more frequent among MSM who reported UAI compared to those who did not (P = 0.001). Use of stimulants before sex was reported by 20% of the MSM, being slightly higher among those who reported UAI (27.0% vs. 15.2%; P = 0.072). Commercial sex was frequent among all MSM (48.4%). After multivariate modeling, the report of sexual abuse or domestic violence (OR = 2.70; 95% CI: 1.08-7.01), commercial sex (OR = 2.28; 95% CI: 1.04- 5.10), the number of male sexual partners (p = 0.039) and exclusively receptive anal intercourse (OR = 0.21; 95% CI: 0.06-0.75) remained associated with UAI. CD4 levels, HIV viral load and antiretroviral therapy were not associated with UAI. Conclusion The UAI prevalence found with negative or unknown HIV status partners points out that other interventions are needed as additional prevention tools to vulnerable MSM. The main factors associated with UAI were a lifetime history of violence, commercial sex and the number of male sexual partners. This clustering of different behavioral, health and social problems in this population reinforce the need of a comprehensive approach on treating and preventing HIV among MSM.