Indigenous participation in every aspect of health research is increasingly recognised as an important element of any research project that aims to improve Indigenous health. Despite the acceptance of its importance, when the concept of 'Indigenous participation' is mentioned, authors are often imprecise as to the nature and purpose of participation, and its relationship to improved health outcomes. This report attempts to bring some clarity to the variety of meanings we might give Indigenous participation in research. For the purposes of stimulating further debate, we identify four distinct, but overlapping, rationales: pragmatic, moral, interventionist, and epistemological. Each has different implications for how Indigenous participation should be implemented and evaluated. More debate on the meanings and purposes of Indigenous participation will contribute to a refined understanding of its potential benefits to health research.