This overview aims to stimulate conceptual and practical discussions to help unlock the full potential of realist evaluation in health systems research. Based on a structured literature search, this review maps how the concepts of realist evaluation are applied in health systems research and which methodological problems are encountered. We found a great diversity in the depth of application of the philosophical concepts, use of terminology and scope of application in the research process. Terms of theory-driven evaluation, theories of change and realist evaluation are often used interchangeably. Diverging views exist regarding the nature of ‘mechanism’ and the difference between mechanism and essential context condition. A lack of methodological guidance was highlighted by many authors. Realist evaluation is slowly gaining traction in health systems research, but more clarity is needed concerning the definitions of mechanisms and context and how the configuration of context, mechanism and intervention can be described and assessed.