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Background: The concept of "mechanism" is central to realist approaches to research, yet research teams struggle to operationalize and apply the concept in empirical research. Our large, interdisciplinary research team has also experienced challenges in making the concept useful in our study of the implementation of models of integrated community-based primary health care (ICBPHC) in three international jurisdictions (Ontario and Quebec in Canada, and in New Zealand)., Methods: In this paper we summarize definitions of mechanism found in realist methodological literature, and report an empirical example of a realist analysis of the implementation ICBPHC., Results: We use our empirical example to illustrate two points. First, the distinction between contexts and mechanisms might ultimately be arbitrary, with more distally located mechanisms becoming contexts as research teams focus their analytic attention more proximally to the outcome of interest. Second, the relationships between mechanisms, human reasoning, and human agency need to be considered in greater detail to inform realist-informed analysis; understanding these relationships is fundamental to understanding the ways in which mechanisms operate through individuals and groups to effect the outcomes of complex health interventions., Conclusions: We conclude our paper with reflections on human agency and outline the implications of our analysis for realist research and realist evaluation.