In the past politics deprived many African children (in particular) in South Africa the opportunity of achieving quality education. This was most especially true in subjects such as mathematics and science. In this research the science teacher-level data from Third International Mathematics and Science Study 1999 (TIMSS’99) were analysed with a view to evaluating the politicized gap between what are viewed as well-functioning and provisioned classrooms (predominantly housing White teachers and White or mixed classes in urban areas) and not well-functioning and poorly provisioned classrooms (largely African teachers and African pupils in peri-urban and rural areas). The data are explored in this article to ascertain and gain insight into similarities and differences in classroom conditions, teacher actions and the relationship between these and pupils’ achievement in science in South African classrooms. Significant differences in achievement were found between classrooms headed by teachers with different racial profiles, where the pupils’ average class science score taught by White teachers was about 300 points more (on a scale with an international mean score of 500 points) than children taught in classrooms by African teachers. Furthermore, the average class science score in rural areas was about 130 points below classes in urban areas. These blatant inequalities contribute to what is believed to be an increasing gap in achievement in science. Whilst these results are not altogether unexpected, there were some interesting results in terms of possible explanatory factors for the gaps in achievement which have ramifications for policymakers.