In this study the authors employed a multilevel analysis procedure in order to examine the pupil and school levels factors that contributed to variation in reading achievement among Grade 6 primary school pupils in 14 southern African school systems (Botswana, Kenya, Lesotho, Malawi, Mauritius, Mozambique, Namibia, Seychelles, South Africa, Swaziland, Tanzania, Uganda, Zambia, and Zanzibar). The data for this study were collected in 2002 as part of a major project known as the Southern and Eastern Africa Consortium for Monitoring Educational Quality (SACMEQ) that sought to examine the quality of education offered in primary schools in these countries. The most important factors affecting variation in pupil achievement across most of these school systems were grade repetition, pupil socioeconomic background, speaking the language of instruction at home, and Pupil age. South Africa, Uganda and Namibia were among the school systems with the largest between-school variation while Seychelles and Mauritius had the largest within-school variation. Low social equity in reading achievement was evident in Mauritius, Seychelles and Tanzania. Policy implications of the findings are discussed.