Men who have sex with Men (MSM) are a key population in the transmission of Human Immunodeficiency Virus (HIV) infection. In Benin, there is a lack of strategic information to offer appropriate interventions for these populations who live hidden due to their stigmatization and discrimination. The objective is to identify contributing factors that affect HIV incidence in the MSM population. Study of a prospective cohort of 358 HIV-negative MSM, aged 18 years and over, reporting having had at least one oral or anal relationship with another man during the last 12 months, prior to recruitment. The monitoring lasted 30 months with a follow-up visit every six months. Univariate analyses and a Cox proportional hazards multivariate regression were used to examine the association between bio-behavioral, socio-demographic and knowledge-related characteristics with HIV incidence. The retention rate for the follow-up of the 358 participants was 94.5%. On the 813.5 person-years of follow-up, 48 seroconversions with an HIV incidence of 5.91 per 100 person-years were observed (95% CI: 4.46-7.85). Factors associated with the high risk of HIV were age (HR = 0.4; 95% CI: 0.2-0.8), living in couple (HR = 0.5 95% CI: 0.2-0.96) and the lack of condom systematic use with a male partner during high-risk sex (HR = 3.9; 95% CI: 1.4-11.1). HIV incidence is high within MSM population and particularly among young people. Targeted, suitable and cost-effective interventions for the delivery of the combination prevention package in an environment free of stigma and discrimination are necessary and vital for reaching the 90x90x90 target.