Abstract Background Inequalities in health have received considerable attention from health scientists and economists. In South Africa, inequalities exist in socio-economic status (SES) and in access to basic social services and are exacerbated by inequalities in health. While health systems, together with the wider social determinants of health, are relevant in seeking to improve health status and health inequalities, those that need good quality health care too seldom get it. Studies on the burden of ill-health in South Africa have shown consistently that, relative to the wealthy, the poor suffer more from more disease and violence. However, these studies are based on selected disease conditions and only consider a single point in time. Trend analyses have yet to be produced. This paper specifically investigates socio-economic related health inequality in South Africa and seeks to understand how the burden of self-reported illness and disability is distributed and whether this has changed since the early 2000s. Methods Several rounds (2002, 2004, 2006, and 2008) of the South African General Household Surveys (GHS) data were used, with standardized and normalized self-reported illness and disability concentration indices to assess the distribution of illness and disability across socio-economic groups. Composite indices of socio-economic status were created using a set of common assets and household characteristics. Results This study demonstrates the existence of socio-economic gradients in self-reported ill-health in South Africa. The burden of the major categories of ill-health and disability is greater among lower than higher socio-economic groups. Even non-communicable diseases, which are frequently seen as diseases of affluence, are increasingly being reported by lower socio-economic groups. For instance, the concentration index of flu (and diabetes) declined from about 0.17 (0.10) in 2002 to 0.05 (0.01) in 2008. These results have also been confirmed internationally. Conclusion The current burden and distribution of ill-health indicates how critical it is for the South African health system to strive for access to and use of health services that is in line with need for such care. Concerted government efforts, within both the health sector and other social and economic sectors are therefore needed to address the significant health inequalities in South Africa.