Otitis media (OM) is one of the most common paediatric illnesses for which medical advice is sought in developed countries. Australian Aboriginal children suffer high rates of OM from early infancy. The resultant hearing loss can affect education and quality of life. As numerous factors contribute to the burden of OM, interventions aimed at reducing the impact of single risk factors are likely to fail. To identify key risk factors and understand how they interact in complex causal pathways, we followed 100 Aboriginal and 180 non-Aboriginal children from birth to age 2 years in a semi-arid zone of Western Australia. We collected demographic, obstetric, socio-economic and environmental data, breast milk once, and nasopharyngeal samples and saliva on seven occasions. Ear health was assessed by clinical examination, tympanometry, transient evoked otoacoustic emissions and audiometry. We considered the conduct of our study in relation to national ethical guidelines for research in Aboriginal and Torres Strait Islander health. After 1 year of community consultation, the study was endorsed by local committees and ethical approval granted. Fieldwork was tailored to minimise disruption to people's lives and we provided regular feedback to the community. We saw 81% of non-Aboriginal and 65% of Aboriginal children at age 12 months. OM was diagnosed on 55% and 26% of routine clinical examinations in Aboriginal and non-Aboriginal children respectively. Aboriginal mothers were younger and less educated, fewer were employed and they lived in more crowded conditions than non-Aboriginal mothers. Sixty-four per cent of Aboriginal and 40% of non-Aboriginal babies were exposed to environmental tobacco smoke. Early consultation, provision of a service while undertaking research, inclusion of Aboriginal people as active members of a research team and appropriate acknowledgement will assist in ensuring successful completion of the research.