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Objective Methodological criteria that characterise ethically sound community-based studies are often described in overviews but are rarely documented in clinical studies. Research investigating the health of Aboriginal Australians is often small-scale, descriptive and largely driven by non-Indigenous people. The ‘community-controlled’ model of research relating to Aboriginal peoples health is a form of ‘participatory’ research that shifts the balance of control towards those being researched. This paper describes the methodological issues and principles that underpin community-controlled health research; their practical application; and encourages their adoption in research involving Indigenous populations.Design Descriptive report of the methods used to conduct the landmark Aboriginal community-controlled multi-centre double-blind randomised controlled clinical ear trial investigating ototopical treatments for chronic suppurative otitis media.Results The characteristics of the community-controlled research model are illustrated under the headings of: setting the research agenda; research project planning and approval; conduct of research; and analysis, dissemination and application of findings.Conclusion The 22 methodological elements which defined the community-controlled design of the ear trial may assist community groups, external research bodies and funding agencies to improve the acceptability, quality and scope of research involving Indigenous peoples. Aboriginal community-controlled organisations are well placed to lead research, which can be interventional and of a high scientific standard without compromising the values and principles of those being researched. With over 120 Aboriginal community-controlled health services (ACCHSs) across Australia, the potential exists for these services to engage in multi-centre research to realise solutions to health problems faced by Indigenous Australians. [ABSTRACT FROM AUTHOR]