Despite high sexually transmitted infection (STI) prevalence in the Pacific, there are limited data on STIs and risk among men who have sex with men (MSM) and transgender people (TG). In 2011, an Integrated Bio-Behavioural Survey recruited self-identified MSM and TG in Port Vila, Vanuatu. Descriptive findings were stratified by sexuality. Among 28 (55%) MSM and 23 (45%) TG, recent anal sex with male partners was more common among MSM (94% vs 71%; P < 0.1), including with casual (47% vs 35%), regular (59% vs 29%) and paying partners (28% vs 12%). MSM more commonly reported lifetime (P < 0.01) and recent sex with female partners (P < 0.01). Reported condom use with any partner type was low. More MSM (35%) than TG (24%) were diagnosed with an STI; previous treatment-seeking behaviour when symptomatic was lower among TG (P < 0.1). Tailored strategies acknowledging differences between MSM and TG are required to reduce STI vulnerability in Vanuatu.