European colonisation had a devastating effect on the health and well-being of indigenous people in Australia. The history of Aboriginal health research has reflected the history of colonisation; research has understandably been viewed with distrust. The need for accurate statistics and improved understanding of health problems is clear, but obtaining them is not easy. In this paper we describe the first stage of a study of the health and well-being of urban young people that was initiated and carried out by the Victorian Aboriginal Health Service (VAHS), a community controlled organisation. This longitudinal study aims to describe the prevalence and incidence of a range of health problems, to explore their interrelated determinants, and to increase the capacity of the VAHS to carry out research. The process of planning and carrying out this study raised a number of interesting ethical, cultural and methodological issues. These issues include the establishment of an appropriate and properly constituted local ethics committee, the difficulty of obtaining a representative sample, the need for ongoing negotiation, attention to language, the use of a subject-generated identity code, and the need to recruit a wide range of peer interviewers. Achievements include a series of community reports of the findings, the establishment of a cohort of young people for a longitudinal study; a shift in attitudes toward research; a strengthened network of young Kooris; increased use of the health service by young people and the establishment of an after-hours clinic service and meeting place for young people. The aim of this analysis of our achievements and constraints is to assist others planning similar research, and to demonstrate the value for process and outcomes of research conducted under Aboriginal community control.