BACKGROUND: On 17 November 2001, less than 900 days after the end of one of the largest population displacements since 1945, the, Kosovo electorate voted for their new self-government. An Assembly was formed in 2001 and a Health Minister, Dr Numan Balic, appointed in March 2002. He has inherited a health service that still reels from many years of neglect while it struggles to implement an ambitious health reform programme. METHODS: An analysis of UNMIK Regulations and available grey literature within Kosovo has formed the basis of material for this article. In addition, the authors collected, by informal interview, the opinions of international and Kosovars actively employed within the health sector. The authors would wish to acknowledge the contribution of Dr Hannu Vuori, Principal International Officer, Ministry of Health, Kosovo for his insight and suggestions. RESULTS: The analysis reveals that the current health system is inequitable and inefficient. The health sector reforms initiated by the international community are desperately needed: it is purported that one-in-three Kosovars cannot afford to access health care when ill. However, the combined legacy of neglect, the current status of the health service and the new Assembly regulations present significant challenges to health reform. CONCLUSIONS: Under the gaze of the newly formed Assembly, as well as the watchful eye of the United Nations Interim Administrative Mission in Kosovo, the Minister will take on the arduous responsibility of governing the Kosovo health sector. In any context implementing reform is difficult, in Kosovo it may be even more so and the international community should not exclusively focus on other world-trouble spots when many challenges remain to be addressed.