There is little known regarding the transmissibility of human papillomavirus (HPV) between different sites in men who have sex with men (MSM) and heterosexual individuals. We conducted a retrospective analysis investigating all new patients attending the Melbourne Sexual Health Centre in Australia between 2002 and 2013. We describe the prevalence and ratio of the first episode of anogenital warts in MSM and heterosexual males and females. The proportion of new MSM clients with anal and penile warts was 4·0% (362/8978) and 1·6% (141/8978), respectively; which gave an anal-to-penile wart ratio of 1:2·6. About 13·7% (1656/12112) of heterosexual males had penile warts and 10·0% (1121/11166) of females had vulval warts, which yielded a penile-to-vulval wart ratio of 1:0·7. Penile–anal transmission has a higher ratio than penile–vulval transmission, suggesting that the anal epithelium may be more susceptible to HPV infection than the vulval epithelium in females; these ratios are important in modelling the control of HPV in MSM.