Recent political developments in South Africa provide many opportunities for the development and extension of health sector links in the Southern African region and the possibility to move away from past hostilities towards a constructive future. The need to address health issues at an inter-governmental level is becoming more urgent as poverty, drought and homelessness take their toll on the health of the region's population. This paper examines the prospects for and problems with regional integration in the health sector. It begins by outlining the historical context of regional health sector links and by discussing crucial issues that have to be addressed in relation to future regional activities. It is suggested that future regional co-operation should be based on a new approach to regional security which seeks to overcome adverse relationships, to encourage collective action and responsibility, non-interference in domestic affairs and peaceful resolution of disputes. The second part of the paper examines areas in the health sector that would benefit from co-operation. These include disease control, nutrition, medicines, health services, health personnel and research and development. Potential problems related to health sector links are explored and possible mechanisms for regional integration in the health sector are briefly considered.