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Background  Longitudinal prospective birth cohort studies are pivotal to identifying fundamental causes and determinants of disease and health over the life course. There is limited information about the challenges, retention, and collection strategies in the study of Indigenous populations. The aim is to describe the follow-up rates of an Australian Aboriginal Birth Cohort study and how they were achieved.    Methods  Participants were 686 babies enrolled between January 1987 and March 1990, born to a mother recorded in the Delivery Suite Register of the Royal Darwin Hospital (RDH) as a self-identified Aboriginal. The majority of the participants (70%) resided in Northern Territory within rural, remote and very remote Aboriginal communities that maintain traditional connections to their land and culture. The Aboriginal communities are within a sparsely populated (0.2 people/ km2) area of approximately 900,000 km2 (347sq miles), with poor communication and transport infrastructures. Follow-ups collecting biomedical and lifestyle data directly from participants in over 40 locations were conducted at 11.4 years (Wave-2) and 18.2 years (Wave-3), with Wave-4 follow-up currently underway.    Results  Follow-ups at 11 and 18 years of age successfully examined 86% and 72% of living participants respectively. Strategies addressing logistic, cultural and ethical challenges are documented.    Conclusions  Satisfactory follow-up rates of a prospective longitudinal Indigenous birth cohort with traditional characteristics are possible while maintaining scientific rigor in a challenging setting. Approaches included flexibility, respect, and transparent communication along with the adoption of culturally sensitive behaviours. This work should inform and assist researchers undertaking or planning similar studies in Indigenous and developing populations.

Challenges and strategies for cohort retention and data collection in an indigenous population: Australian Aboriginal Birth Cohort