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Introduction: In Australia, Aboriginal youth are disproportionately represented in juvenile detention centres. We assessed the prevalence of sexually transmissible infections (STIs) and blood-borne viruses (BBVs) identified by an Aboriginal Health Worker (AHW)-led screening program delivered to male detainees of a rural juvenile detention centre., Methods: A retrospective review of first screening visit data was performed. Demographic and behavioural data were collected and the prevalence of STI/BBV was assessed., Results: Over a 4-year period to November 2004, 101 screens on new medium-to-long-term detainees were performed. The median age of participants was 17 years (range 14-20) and 87% were Aboriginal. Most reported multiple lifetime sexual partners (mean 14, range 0-60) and a minority had used a condom for the last episode of vaginal intercourse. Injecting drug use and non-professional tattoos or piercings were both reported by over one-third of participants, with over 80% reporting previous incarceration. One-quarter of those screened were newly diagnosed with one or more STI/BBV. The most common infection identified was urethral chlamydia (prevalence 16.3%, 95% confidence interval 10.0-25.5%), although the prevalence of newly diagnosed syphilis, hepatitis B and hepatitis C were each over 5%. Many participants remained susceptible to hepatitis B., Conclusion: An AHW-led STI/BBV screening program identified a large number of asymptomatic and previously undiagnosed infections in this group of young male detainees. Such an education and screening program using skilled Aboriginal staff not affiliated with the correctional system could have a substantial impact on the prevalence of STI/BBV among juvenile detainees.