Gonorrhoea and chlamydia cases have been rising among gay, bisexual and other men who have sex with men (MSM) over the last decade. The majority of cases are extragenital and occur at the oropharynx and anorectum. The aim of this narrative review was to review the risk factors and mode of transmission for gonorrhoea and chlamydia at the oropharynx and anorectum among MSM. New evidence suggests that oropharyngeal gonorrhoea can be transmitted by kissing in addition to through the established route of condomless oral sex; and anorectal gonorrhoea can be acquired when saliva is used as a lubricant for anal sex and rimming in addition to the established route of condomless penile-anal sex in MSM. In contrast, condomless penile-anal sex remains the major route for chlamydia transmission. Substantial transmission of gonorrhoea may occur with practices other than the established routes of condomless oral and/or anal sex and hence condoms may not be effective in preventing gonorrhoea transmission to extragenital sites. In contrast, condoms are effective for chlamydia control because it is mainly transmitted through condomless penile-anal sex. Novel interventions for gonorrhoea that reduce the risk of transmission at extragenital site are required. © 2019 The Authors. Journal of the International AIDS Society published by John Wiley & Sons Ltd on behalf of the International AIDS Society.