M genitalium was less common than C trachomatis and N gonorrhoeae in MSM attending male-only saunas and was most often detected as an asymptomatic rectal or a urethral infection but was absent from the pharynx. To inform STI screening strategies in MSM, more data are needed to understand how common M genitalium infection is in urethral and non-urethral sites in MSM, and how it contributes to clinical symptoms.