Managers and staff in primary health care partnerships in local catchments, particularly in regional areas, are periodically required to work collaboratively to set health priorities. Setting priorities involves making decisions about which health needs are most important and what programs will be funded to address them. There is no universally agreed set of decision-making rules for setting priorities. Dominant approaches prioritise health economics, and have favoured expert knowledge drawn from technical-rational methodologies rather than consumer involvement and community action. However, research reveals that setting priorities is a complex, value laden, contested process buffeted by competing objectives and political interests. As such, an interdisciplinary, collaborative approach is called for. Using reflective practice from a priority setting project for a primary care partnership in a local, regional catchment in Victoria, Australia, a conceptual framework for priority setting is presented that identifies 13 interconnected factors spanning economic, political, policy, epidemiological, moral, evidentiary and evaluative domains. This interdisciplinary framework extends current knowledge about the considerations and trade-offs in setting priorities among collaborating primary health care agencies. It offers a potentially valuable heuristic tool for healthcare decision-makers in rural areas.