BACKGROUND: Seven years after the end of war in Kosovo, Final Status Negotiations have begun to determine the long-term political future of the province. This article provides an overview of the present situation regarding ethnic groups and their relations in Kosovo's health care system that might be helpful in preparing for the array of potential ramifications and repercussions that could arise at the conclusion of the negotiations. METHODS: A review of the literature (including grey) was performed, and 16 interviews and two focus groups with key informants were conducted in Kosovo during October and November 2004. In addition, six informal discussions were held in-person or by telephone in London. Information collected in 2004 was re-confirmed and partially updated in October and November 2005, when three additional interviews were conducted in Kosovo. RESULTS: Ongoing ethnic tensions in Kosovo, mainly between the Albanian and Serb populations, perpetuate a rigidly segregated health care system. Some other minority communities, such as the Roma, Ashkali and Egyptians, are afflicted by the double burden of getting caught up in the middle of these ethnic disputes and at the same time suffering from poverty and discrimination. CONCLUSION: While efforts have been put forward to promote peace-building within Kosovo's post-war health sector, very little progress has been achieved in fostering ethnic integration, reconciliation, cooperation or even co-existence. This failure reflects Kosovo's broader unresolved inter-ethnic problems. Final Status Negotiations are one of the last opportunities for the international community to address the problems of ethnic segregation in the province.