This study examined the effects of selected classroom factors (the emphasis on a student-centred approach, the shortage of instructional resources and homework) on the science and mathematics achievement of Jordanian eighth graders using data from the Trends in International Mathematics and Science Study of 2007. The analytical model also included some student-level factors such as the highest level of parents' education and attitudes towards subject. A hierarchical linear model was used to analyse the data; a significance level of 0.05 was used. The results of this study showed that there was a significant variation in science and mathematics achievement among Jordanian classes/schools. About 20% of the variation in achievement was found among the Jordanian schools. The results showed that the effects of the selected class-level factors were not stable across science and mathematics. For example, the shortage of instructional resources negatively affected the mathematics achievement of the Jordanian eighth graders, but had no significant effect on science achievement. In short, it could be concluded that subject matter matters because the same factors operated differently in explaining the variance in science and mathematics. Some implications for researchers, policy-makers and school personnel are offered to improve science and mathematics achievement. (Contains 3 tables.)