Background Despite the growth of biomedical research in South Africa, there are few insights into the operation of Research Ethics Committees (RECs) in this setting. We investigated the composition, operations and training needs of health RECs in South Africa against the backdrop of national and international guidelines. Methods The 12 major health RECs in South Africa were surveyed using semi-structured questionnaires that investigated the composition and functions of each REC as well as the operational issues facing committees. Results Health RECs in SA have an average of 16 members and REC members are predominantly male and white. Overall, there was a large discrepancy in findings between under-resourced RECs and well resourced RECs. The majority of members (56%) are scientists or clinicians who are typically affiliated to the same institution as the health REC. Community representatives account for only 8% of membership. Training needs for health REC members varied widely. Conclusion Most major health RECs in South Africa are well organized given the resource constraints that exist in relation to research ethics in developing countries. However, the gender, racial and occupational diversity of most of these RECs is suboptimal, and most RECs are not constituted in accordance with South African guidelines. Variability in the operations and training needs of RECs is a reflection of apartheid-entrenched influences in tertiary education in SA. While legislation now exists to enforce standardization of research ethics review systems, no provision has been made for resources or capacity development, especially to support historically-disadvantaged institutions. Perpetuation of this legacy of apartheid represents a violation of the principles of justice and equity.