Little is known about the incidence of bacterial sexually transmitted infections (STIs) among HIV-infected versus HIV-uninfected adolescents. This secondary analysis of a national, multisite study included adolescents aged 12-18 years who were behaviourally HIV-infected (n = 346) or HIV-uninfected but at-risk (n = 182). Incidence rates of bacterial STIs (gonorrhoea, chlamydia [CT] and trichomonas [TV; women]) were calculated using Poisson modelling. Factors associated with incident STIs were explored using Cox proportional hazards modelling. HIV-infected versus HIV-uninfected women had higher TV incidence (1.3 versus 0.6/100 person-months; P = 0.002). HIV-uninfected versus HIV-infected women had higher CT incidence (1.6 versus 1.1/100 person-months; P = 0.04). Among women, demographic, behavioural and HIV-related factors were associated with incident STIs. Among men, there were no differences in incident STIs. In this first analysis comparing STI incidence between HIV-infected and HIV-uninfected adolescents, bacterial STI incidence among women significantly differed by HIV status, and factors associated with incident STIs varied by STI and HIV status.