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Introduction The health of Indigenous Australians is worse than that of other Australians. Most of the determinants of health are preventable and the poor health outcomes are inequitable. The Australian Government recently pledged to close that health gap. One possible way is to improve the priority setting process to ensure transparency and the use of evidence such as epidemiology, equity and economic evaluation. The purpose of this research was to elicit the perceptions of Indigenous and non-Indigenous decision-makers on several issues related to priority setting in Indigenous-specific health care services. Specifically, we aimed to: 1. identify the criteria used to set priorities in Indigenous-specific health care services; 2. determine the level of uptake of economic evaluation evidence by decision-makers and how to improve its uptake; and 3. identify how the priority setting process can be improved from the perspective of decisionmakers. Methods We used a paper survey instrument, adapted from Mitton and colleagues' work, and a faceto- face interview approach to elicit decision-makers' perceptions in Indigenous-specific health care in Victoria, Australia. We used mixed methods to analyse data from the survey. Responses were summarised using descriptive statistics and content analysis. Results were reported as numbers and percentages. Results The size of the health burden; sustainability and acceptability of interventions; historical trends/patterns; and efficiency are key criteria for making choices in Indigenous health in Victoria. There is a need for an explicit priority setting approach, which is systematic, and is able to use available data/evidence, such as economic evaluation evidence. The involvement of Indigenous Australians in the process would potentially make the process acceptable. Conclusions An economic approach to priority setting is a potentially acceptable and useful tool for Aboriginal Community Controlled Health Services (ACCHS). It has the ability to use evidence and ensure due process at the same time. The use of evidence can ensure that health outcomes for Indigenous peoples can be maximised - hence, increase the potential for 'closing the gap' between Indigenous and other Australians. [ABSTRACT FROM AUTHOR]