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Mycoplasma genitalium (M. genitalium) is a recently recognised and important sexually transmitted infection among men who have sex with men (MSM). The role of oral sex, rimming, and kissing on M. genitalium transmission in MSM is unclear. We created four deterministic susceptible-infectious-susceptible epidemic models to examine the role that different sexual behaviours play in transmitting M. genitalium at the oropharynx, urethra anorectum among men who have sex with men in Australia. Our results suggest that oral and anal sex without other sexual practices (model 1) replicate well single site infection at the oropharynx, urethra and anorectum and also multi-site infection. If kissing or rimming are added to model 1 (i.e., model 2–4) no substantial improvements in the calibration of the models occur. Model 1 estimates that 3.4% of infections occur at the oropharynx, 34.8% at the urethra and 61.8% at the anorectum. Model 1 also estimates that the proportion of incident M. genitalium transmitted by anal sex was 82.4%, and by oral sex was about 17.6%. Our findings could provide an enhanced understanding of M. genitalium transmission in MSM, thus providing insights into what sexual practices contribute most to transmission.