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Background Sexual assault is a violent crime that affects men, women, and children of all ages. Sexually transmitted infections (STIs) may be transmitted during sexual assault. This study was aimed at finding the prevalence of sexually transmitted infections in potentially sexually abused children and adolescent in Ibadan. Methods This is a descriptive cross-sectional survey of Children and adolescents referred for possible evaluation of sexual abuse at Special Treatment Clinic, University College Hospital, Ibadan between January 2006 and December 2008. Urethral, Endocervical and high vaginal swabs were collected to establish diagnosis after clinical examination and informed consent. Results There were 18 children and adolescents with a mean age of 9.75 years (SD=5.78; range 2–18 years). About 66.7 % (12) had various STIs. The male to female ratio was 1:8. Five (27.8%) had physical evidence of sexual assault at presentation, 4 (22.2%) of which had hyperaemic labia and one had torn hymen. 12 (66.7%) presented with vaginal discharge syndrome. The most common STI diagnosed was genital warts (22.2.0%). Other STIs diagnosed were vaginal candidiasis (16.7%), bacterial vaginosis (11.1%) and HIV (5.6%). There was no statistical significance between HIV infection and other STIs (p>0.05). Conclusion Our study revealed high prevalence of sexually transmitted infections among the sexually abused children and adolescents. Screening for infection should be mandatory in presumed sexually abused girls with vaginal discharge and ideally should be undertaken in all children presenting at STI clinics for evaluation of sexual abuse.