With mounting evidence that health problems are related to social inequalities, health researchers increasingly need to engage with disadvantaged and marginalised groups. These groups can present specific challenges to conventional research method. This paper reflects on the need for health researchers to meet these challenges in order to gain a deeper understanding of the ways in which social disadvantage affects people's health, and to develop appropriate interventions for those groups. Models of collaborative, participatory and action research are defined on a continuum. The value of a collaborative participatory approach to health research is discussed. Key processes in collaboration are outlined, and some of the methodological tensions and ethical issues that arise when using such an approach are addressed. The recognition that power is directly related to knowledge lies at the heart of the collaborative participatory research project. Collaborative participatory research offers a strategy that embraces self-determination, encourages and even demands ongoing consultation and negotiation, and provides opportunities for capacity-building and empowerment in the communities involved in the research. Nowhere is such a strategy more needed in Australia today than for research with Indigenous communities.