Discrimination due to sexual orientation (DDSO) has an important association with health outcomes among men who have sex with men (MSM). This study aimed to analyze factors associated with DDSO among MSM in 12 Brazilian cities. This is a cross-sectional study with 4,176 MSM participants recruited in 2016 which used a respondent-driven sampling method in 12 Brazilian cities. DDSO levels were previously identified by a latent class analysis based on 13 variables from the discrimination section. An ordinal logistic regression was used to assess associations with these DDSO levels, and weighted ordinal odds ratios (OR) and their respective 95% confidence intervals (95%CI) were estimated using Gile's estimator. Most participants were young (< 25 years old) black or of mixed-race (pardo), single individuals who had a religious affiliation, primary or incomplete secondary education, and a high and average socioeconomic status. More than half (65%) reported DDSO in the 12 months prior to this study. We observed an independent association among the four latent DDSO classes and the following variables: age < 25 years old (OR = 1.66; 95%CI: 1.21-2.27), white skin color (OR = 1.43; 95%CI: 1.02-2.01), history of sexual (OR = 2.33; 95%CI: 1.58-3.43) and physical violence (OR = 3.08; 95%CI: 2.11-4.49), disclosure of their sexual orientation as MSM to their fathers (OR = 2.00; 95%CI: 1.47-2.72), experienced suicidal ideation in the two weeks prior to this study (OR = 2.09; 95%CI: 1.46-2.98), and use of any illicit drugs in the last six months (OR = 1.61; 95%CI: 1.19-2.18). Our results indicate that contextual factors may contribute to high DDSO levels among MSM in Brazil. Public health policies toward human rights surveillance and protection among MSM must be urgently addressed.