The roots of a dysfunctional health system and the collision of the epidemics of communicable and non-communicable diseases in South Africa can be found in policies from periods of the country's history, from colonial subjugation, apartheid dispossession, to the post-apartheid period. Racial and gender discrimination, the migrant labour system, the destruction of family life, vast income inequalities, and extreme violence have all formed part of South Africa's troubled past, and all have inexorably affected health and health services. In 1994, when apartheid ended, the health system faced massive challenges, many of which still persist. Macroeconomic policies, fostering growth rather than redistribution, contributed to the persistence of economic disparities between races despite a large expansion in social grants. The public health system has been transformed into an integrated, comprehensive national service, but failures in leadership and stewardship and weak management have led to inadequate implementation of what are often good policies. Pivotal facets of primary health care are not in place and there is a substantial human resources crisis facing the health sector. The HIV epidemic has contributed to and accelerated these challenges. All of these factors need to be addressed by the new government if health is to be improved and the Millennium Development Goals achieved in South Africa.