Most health and substance abuse programs for indigenous peoples in Australia are funded by government. Over the past decade there have been calls for greater accountability in the conduct of these programs. Initial attempts focused on the development of standardised performance indicators; an approach that has been roundly criticised on both political and methodological grounds. Recently, some government agencies have sought to identify culturally appropriate models for the evaluation of programs for indigenous peoples. In a comparative review of the evaluation of indigenous programs in Australia and Canada, conducted for the Western Australian Aboriginal Affairs Department, the authors were not able to identify any generally applicable models. However, this literature review and our own research and experience in working with Aboriginal community organisations have identified a number of principles that should be an essential part of any attempts to evaluate health and substance abuse programs for indigenous peoples. Underlying these principles is the realisation that evaluation is not a politically or ideologically neutral activity. Theoretical and methodological considerations of the evaluation process must take into account the very real differences between the agendas of indigenous peoples and those who seek to evaluate programs for them.