We estimated the prevalence of sexual violence (SV) experience among men who have sex with men (MSM) in Brazil and identified its associated risk factors. We recruited 3859 MSM through respondent driven sampling. A multivariable hierarchical analysis was performed using an ecological model. The prevalence of having ever experienced SV was 15.9 % (95 % confidence interval [CI] 14.7-17.1). SV experience was independently associated with discrimination due to sexual orientation (odds ratio [OR] 3.05; 95 % CI 2.10-4.42), prior HIV testing (OR 1.81; 95 % CI 1.25-2.63), ≤14 years at first sex (OR 1.86; 95 % CI 1.28-2.71), first sex with a man (OR 1.89; 95 % CI 1.28-2.79), presenting STI symptoms (last year) (OR 1.66; 95 % CI 1.12-2.47), and having suicidal ideas (last 6 months) (OR 2.08; 95 % CI 1.30-3.35). The high levels of SV against MSM in Brazil place them at a markedly higher risk of SV than the general population. Homophobic prejudice is the strongest determinant of SV and urgently needs to be included at the forefront of the national response to SV.