Background: Sub-Saharan Africa is a region of both high HIV and anal cancer incidence. We conducted the first national study in Togo to assess HPV, HIV and other Sexually Transmitted Infections (STIs) prevalence among Men having Sex with Men (MSM). Methods: A multicentric cross-sectional study was conducted among MSM recruited in four Togolese cities based on the respondent-driven sampling method. Socio-demographic characteristics and sexual behaviors were recorded using a standardized questionnaire. Anal swabs were collected to test HPV, HSV-1/2 and seven anal STIs. HIV, Syphilis and HBV were screened with rapid tests. Results: 207 MSM were recruited, showing HIVand high-risk HPV (hrHPV) overall prevalence of 26.1% and 44.9%, respectively. Most common hrHPV types were HPV35 (15.0%) and HPV16 (13.0%). Prevalence of hrHPV and multiple HPV infections were higher among HIV-positive than among HIV-negative MSM (85.2% versus 30.7%, p<10-5 and 85.2% versus 28.7%, p<10-5, respectively). Other STIs, except HBV, were also more prevalent among HIV-positive MSM (N.gonorrhoeae, p=0.03; M.genitalium, p=0.04; HSV-2, p=0.001 and a trend for C.trachomatis, p=0.06). In multivariate analysis, HIV infection (aOR: 10.1, 95%CI: 4.0-25.6), living in Lome (2.8, 1.1-7.1), HSV-2 anal excretion (26.7, 2.9-244.3), anal C.trachomatis (11.7, 2.3-58.9) and M.genitalium infection (9.6, 3.1-29.9) were associated with increased risk of anal hrHPV infection. All participants with anal N.gonorrhoeae infection were infected with at least one hrHPV. Conclusions: We report a high-burden of anal STIs with an unusual hrHPV types distribution among MSM, highlighting the critical need of implementation of a national strategy regarding prevention of STIs and vaccination against Papillomavirus.< Réduire