Community-based healthcare organisations manage competing, and often conflicting, priorities. These conflicts can arise from the multiple roles these organisations take up, and from the diverse range of stakeholders to whom they must be responsive. Often such conflicts may be titled conflicts of interest; however, what precisely constitutes such conflicts and what should be done about them is not always clear. Clarity about the duties owed by organisations and the roles they assume can help identify and manage some of these conflicts. Taking divisions of general practice in Australia as an example, this paper sets out to distinguish two main types of conflicts of interest, so that they may be more clearly identified and more effectively managed.