IntroductionPrenatal alcohol exposure can cause lifelong disability, including physical, cognitive and behavioural deficits, known as fetal alcohol spectrum disorders (FASD). Among individuals with FASD, engagement with justice services is common. Little is known about the prevalence of FASD among young people engaged with the Australian justice system. This study aims to establish FASD prevalence among sentenced young people in detention in Western Australia (WA), and use the findings to develop a screening tool for use among young people entering detention. Translation of these results will guide the management and support of young people in detention and will have significant implications on the lives of young people with FASD and the future of Australian youth justice services.Methods and analysisAny sentenced young person in WA aged 10–17 years 11 months is eligible to participate. Young people are assessed for FASD by a multidisciplinary team. Standardised assessment tools refined for the Australian context are used, acknowledging the language and social complexities involved. Australian diagnostic guidelines for FASD will be applied. Information is obtained from young people, responsible adults, teachers and custodial officers. Individualised results and management plans for each young person are communicated to the young person and responsible adult. Prevalence of FASD will be reported and multivariate methods used to identify variables most predictive of FASD and to optimise the predictive value of screening.Ethics and disseminationApprovals have been granted by the WA Aboriginal Health Ethics Committee, University of WA Human Research Ethics Committee, Department of Corrective Services, and Department for Child Protection and Family Support. Anonymised findings will be disseminated through peer-reviewed manuscripts, presentations and the media. Extensive consultation with stakeholders (including government agencies, detention centre staff, community service providers, the young people and their families or carers) will be ongoing until findings are disseminated and translated.