This paper reports on an epidemiological study of common mental health and substance abuse problems in a historically disadvantaged urban and rural community in South Africa. In the rural Limpopo Province of South Africa, and in a peri-urban township near Cape Town, self-report instruments were used in two random population samples and among respondents at primary care and traditional healer settings, to assess common mental health problems, substance abuse problems and associated problems in social functioning. A high prevalence of mental health and substance abuse problems was observed in both communities, with highest rates in the peri-urban township. Even higher prevalences were found among respondents at primary health care or traditional healers. The study shows that mental health and substance abuse problems constitute a considerable burden of disease among disadvantaged communities in South Africa. The study further underscores the integral role of traditional healers in the mental health care system.