In this essay, we give an overview of the relationships between the design and structure of health systems, health service provision and utilisation, and inequalities in population health. This shows the added value of combining health systems, health services and population health research, areas that have become siloed. In so doing, we hope to create awareness among researchers to look beyond the boundaries of their own field and promote multidisciplinary collaboration. We start with an answer to the question of the relationship between healthcare system structure and equality in population health and highlight the intermediate steps necessary to understand how this relationship works. We then identify the research and policy added value of combining health systems, health services and population health research. To fill gaps in current knowledge, we propose elements of a research agenda and discuss the necessary conditions for integration and collaboration between the three fields of research.