Previous studies on the role of the school in influencing attainment in South African schools have concluded that the inequalities which are known to exist in these are still largely due to the legacy of the Apartheid system. More recently, policy focus has been on narrowing the gap between the attainment of different socio-economic groups by addressing the inequality in school resource levels and facilities. The work presented here investigates which pupil background, school context and school resource (human and physical) factors affect individual academic attainment by developing separate multilevel models for individual learners of similar socio-economic status. This approach allows for the possibility that different in- and out-of-school factors combine to explain the differences in attained mathematics and reading scores of Grade 6 pupils participating in the SACMEQ II survey in 2000, and that this could be dependent on the socio-economic status of the individual learner. It is argued that policy focus should be wider than just resourcing levels. The evidence points to the need to additionally target deprived, mainly rural, neighbourhoods and develop interventions and alternative strategies to overcome some of the acute social disadvantages that pupils, especially from the lowest socio-economic status, bring with them into school. These include poor nutrition, lower fluency levels in the language of instruction used in schools and higher chances of living away from home in order to be schooled. (Contains 4 notes, 4 tables, and 3 tables.)