In the TIMSS 1999 study South African data are available at both school and teacher level, in addition to the student level data permitting researchers to explore the reasons for the poor South African performance in science. Where in earlier research factors influencing mathematics achievement in South Africa were studied (Howie, 2002), this paper will focus on science achievement. Questions on class level regarding the teacher characteristics, the implemented curriculum, language used in the classroom and instruction will be investigated in relation to science achievement. As more than 80% of the South African TIMSS 1999 sample comprised schools, which are disadvantaged in terms of human and physical resources, it is critical that an analysis of the data from the science teachers' questionnaire is done to ascertain the effect of the conditions within these disadvantaged schools on the students' science performance. Partial Least Square analysis is used to analyse both the indirect and direct effects of school-level variables on achievement. In the final part of the paper, the results for science achievement will be discussed in relation to the findings for mathematics achievement.