While conflict continues to threaten health development in many countries, relative peace has been secured in others. The transition from war to peace carries important political and economic opportunities for the reappraisal of social policy in general, and of health policy in particular. The health systems of countries recovering from prolonged periods of conflict often carry a double burden: the inheritance of an inappropriate and unaffordable health system developed in the pre-conflict era, and the particular, long-term effects of conflict on health and health services. This paper reports on the particular policies designed to rehabilitate the Ugandan health system, and argues that they exacerbated, rather than alleviated, the health crisis inherited in 1986. In this way they posed a third burden. By analyzing the context and process of policy formulation in the immediate post-conflict period, it explores the rationale which lay behind the adoption of these policies and identifies potential strategies for strengthening policy development in these unstable, resource-poor and health-deprived situations.