Men who have sex with men (MSM) are a population at risk of contracting both HIV and hepatitis B virus (HBV). The objective of this study was to assess the prevalence of these diseases and the factors associated with them among MSM in Togo in 2017. This cross-sectional study took place in eight major cities in Togo from August through September, 2017. MSM aged 18 years and older were recruited with the respondent-driven sampling method. Data on sexual behavior were collected with a standardized questionnaire. Rapid tests were used to screen for HIV and HBV. In all, 678 MSM with a median age of 23 years (interquartile range: 21-26) were recruited, 68.7% of them living in Lomé, the capital of Togo. The prevalence of HIV was 22.0% (95% confidence interval [95% CI] 18.9-25.3) and that of HBV 7.1% (95% CI 5.3-9.3). Seven (1.0%) MSM were co-infected with HIV and HBV. Age, place of residence, living with a male partner, the number of male partners in the 12 months before the study, and history of HIV testing were associated with HIV infection (P<0.05). Age and living in Lomé were associated with HBV infection (P<0.05). The results of this study highlight the importance of focusing response efforts on populations at risk of contracting STIs through routine screening and vaccination.