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Background: There is considerable potential for health research to contribute to improved health services, programs, and outcomes; the policies of health research funding agencies are critical to achieving health gains from research. The need for research to better address health disparities in Indigenous people has been widely recognised. This paper: (i) describes the policy changes made by the National Health and Medical Research Council (NHMRC) from 1997 to 2002 to improve funding of Aboriginal health research (ii) examines catalysts for the policy changes (iii) describes the extent to which policy changes were followed by new models of research and (iv) outlines issues for Indigenous health policy in the future. Methods: This study had two parts: (i) semi-structured interviews were conducted over a four - month period with seven individuals who played a leading role in the policy changes at NHMRC during the period 1997-2002, to describe policy changes and to examine the catalysts for the changes; (ii) a case study was undertaken to evaluate projects by recipients of NHMRC People Support awards and NHMRC Capacity Building Grants in Population Health Research to examine the types of research being undertaken five years after the policy changes were implemented. The proposals of these researchers were assessed in terms of whether they reported intending to: evaluate interventions; engage Indigenous community members and organisations; and build research capacity among Indigenous people. Results: Seven policy changes over a period of five years were identified, including those to: establish an ethical approach to working with Indigenous people; increase the influence of Indigenous people within NHMRC; encourage priority research directed at improving Indigenous health; and recognise Aboriginal and Torres Strait Islander health research as a priority area including a commitment to an expenditure target of 5% of annual funds. Seven catalysts for this change were identified. These included: a perceived lack of effective response to the health needs of Indigenous people; a changed perception of the role of NHMRC in encouraging research to maximise health gains; and leadership within the organisation. The case study analysis demonstrated that 45% of all People Support recipients intend to engage Indigenous community members and organisations in consultation, 26% included an evaluation of an intervention and two (6.5%) were granted to an individual from an Indigenous background. Six of seven Population Health Capacity Building Grants that were awarded to study Indigenous health between 2004 and 2006 included an intervention component; these grants supported 34 researchers from Indigenous backgrounds. Conclusion: NHMRC made significant policy changes from 1997 to 2002 to better support Indigenous health as a result of external pressure and internal commitment. The policy changes have made some progress in supporting better research models particularly in improving engagement with Indigenous communities. However, there remains a need for further reform to optimise research outcomes for Indigenous people from research. [ABSTRACT FROM AUTHOR]