This study uses the 1996 Census and the 1998 Demographic and Health Survey (DHS) to investigate the level of and trend in infant and child mortality and their covariates in South Africa. Census estimates of childhood mortality are higher than those from the DHS. Analysis suggests that the former overestimate mortality while the latter are probably slightly too low. Both inquiries document a reversal of the trend toward lower mortality in the 1990s. Under-five mortality increased by about a third during the five years up to early 1998. By then the infant mortality rate was about 55 per 1000 and under-five mortality 72 per 1000. Other factors may explain the tapering off of the decline in mortality after the late 1980s but AIDS deaths account for its increase. Inequalities in childhood mortality between population groups, rooted in past discriminatory apartheid policies, shrank between the late-1970s and mid-1990s. However, they remain substantial and are largely unaccounted for by province, metropolitan residence and inter-group differences in mothers’ education. The HIV/AIDS epidemic is likely to offset the beneficial impact of post-apartheid pro-poor policies and may exacerbate racial differences in childhood mortality in South Africa. There is an urgent need to improve the routine collection of statistics to monitor child mortality so as to assess progress towards the Millennium Development Goals and track inequalities.