Background Brazil has the largest population of individuals living with HIV/AIDS in Latin America, with a disproportional prevalence of infection among gays, bisexuals and other men who have sex with men (MSM). Of relevance to prevention and treatment efforts, Brazilian MSM from different regions may differ in behaviors and risk perception related to HIV.Methods We report on MSM living in 29 different cities: 26 Brazilian state capitals, the Federal District and two large cities in São Paulo state assessed in three web-based surveys (2016-2018) advertised on Grindr, Hornet and Facebook. Using logistic regression models, we assessed factors associated with high-risk behavior and high HIV perceived risk.Results A total of 16,667 MSM completed the survey. Overall, MSM from the North and Northeast were younger, more black/mixed-black, of lower income and lower education compared to MSM from the South, Southeast and Central-west. Though 17% had never tested for HIV (with higher percentages in the North and Northeast), condomless receptive anal sex (previous 6 months) and high-risk behavior as per HIV Incidence Risk scale for MSM were observed for 41% and 64%, respectively. Sexual behaviors and HIV perceived risk had low variability by city. Younger age, being gay/homosexual, having a steady partner, binge drinking, report of STI and ever testing for HIV increased the odds of high-risk behavior. In contrast, younger age and having a steady partner decreased the odds of high HIV perceived risk, while report of STI most strongly increased the odds of high HIV perceived risk. All variables that serve as proxies for low socio-economic status (black/mixed-black race, low income and low education) were associated with increased odds of high HIV perceived risk. Awareness and willingness to use PrEP increased from 2016 to 2018 in most cities.Conclusions Overall, MSM socio-demographic characteristics were heterogeneous among Brazilian cities, but similarities were noted among the cities from the same administrative region with a marked exception of the Federal District not following the patterns for the Central-West. The observed dissonance between sexual behavior and HIV perceived risk may be a barrier to effective PrEP implementation.