Background. The objective was through an analysis of longitudinal data from the DepIST-H cohort to estimate the incidence, describe the dynamics and factors associated with CT/NG infection in MSM in Togo. Methods. A total of 200 MSM in Lome, Togo, were included in the ANRS I MIE 12400/DepIST-H cohort, half living with HIV. After inclusion in the study, participants received follow-up clinical visits at 6 and 18 months, and laboratory tests were performed at baseline (M0) and at 12 and 24 months (M12 and M24). PCR tests for CT and NG were performed from pharyngeal, anal and urine samples collected using the Xpert(R) CT/GC kit (Sunnyvale, CA, USA). To identify the factors associated with anal bacterial STIs, offset term Poisson regression models were performed. Results. Among 200 MSM (median age 24 years), CT and NG incidence rates were high ({approx}22 cases per 100 person-years), particularly at the anal site. Multiple partners significantly increased anal NG incidence (aIRR 2.35). Anal NG incidence was significantly lower among participants with income-generating activity (aIRR 0.57). Trends suggested higher anal CT and NG incidence in the presence of pharyngeal infection, but associations were not statistically significant Conclusion. This study confirms that MSM remain highly exposed to STIs in Togo and highlights the need to strengthen prevention efforts within this population. Postexposure doxycycline prophylaxis and multisite pooled-sample screening represent promising avenues to strengthen prevention efforts within these populations.