Background: This paper describes the development of a model of Comprehensive Primary Health Care (CPHC) applicable to the Australian context. CPHC holds promise as an effective model of health system organization able to improve population health and increase health equity. However, there is little literature that describes and evaluates CPHC as a whole, with most evaluation focusing on specific programs. The lack of a consensus on what constitutes CPHC, and the complex and context-sensitive nature of CPHC are all barriers to evaluation. Methods. The research was undertaken in partnership with six Australian primary health care services: four state government funded and managed services, one sexual health non-government organization, and one Aboriginal community controlled health service. A draft model was crafted combining program logic and theory-based approaches, drawing on relevant literature, 68 interviews with primary health care service staff, and researcher experience. The model was then refined through an iterative process involving two to three workshops at each of the six participating primary health care services, engaging health service staff, regional health executives and central health department staff. Results: The resultant Southgate Model of CPHC in Australia model articulates the theory of change of how and why CPHC service components and activities, based on the theory, evidence and values which underpin a CPHC approach, are likely to lead to individual and population health outcomes and increased health equity. The model captures the importance of context, the mechanisms of CPHC, and the space for action services have to work within. The process of development engendered and supported collaborative relationships between researchers and stakeholders and the product provided a description of CPHC as a whole and a framework for evaluation. The model was endorsed at a research symposium involving investigators, service staff, and key stakeholders. Conclusions: The development of a theory-based program logic model provided a framework for evaluation that allows the tracking of progress towards desired outcomes and exploration of the particular aspects of context and mechanisms that produce outcomes. This is important because there are no existing models which enable the evaluation of CPHC services in their entirety.