This article describes some of the crucial theoretical, methodological and practical issues that need to be considered when evaluating Health in All Policies (HiAP) initiatives. The approaches that have been applied to evaluate HiAP in South Australia are drawn upon as case studies, and early findings from this evaluative research are provided. The South Australian evaluation of HiAP is based on a close partnership between researchers and public servants. The article describes the South Australian HiAP research partnership and considers its benefits and drawbacks in terms of the impact on the scope of the research, the types of evidence that can be collected and the implications for knowledge transfer. This partnership evolved from the conduct of process evaluations and is continuing to develop through joint collaboration on an Australian National Health & Medical Research Council grant. The South Australian research is not seeking to establish causality through statistical tests of correlations, but instead by creating a ‘burden of evidence’ which supports logically coherent chains of relations. These chains emerge through contrasting and comparing findings from many relevant and extant forms of evidence. As such, program logic is being used to attribute policy change to eventual health outcomes. The article presents the preliminary program logic model and describes the early work of applying the program logic approach to HiAP. The article concludes with an assessment of factors that have accounted for HiAP being sustained in South Australia from 2008 to 2013.