We report two instances of urethral-to-rectal transmission of Mycoplasma genitalium (MG) in men who have sex with men (MSM) couples. Such clear epidemiological correlation has to our knowledge not been published before. The urethral infections led to clinical symptoms, but the rectal infections did not. The rectum might serve as a reservoir for MG in MSM, but there is also some evidence from the literature that MG can cause proctitis. Our finding raises important questions about the role of MG as a pathogen among MSM. Any correlation with HIV transmission risk is currently unknown and needs further research.