Gender differences in science amongst year 8 students in Australia in TIMSS 2003 were a surprise, given two decades of programs designed to increase girls’ participation levels in science. This study examines student and school-level characteristics simultaneously using hierarchical linear modelling to estimate the ability of each to explain gender differences in science achievement for students with differing socioeconomic backgrounds. Using separate datasets for low and high socioeconomic background schools, adjusting for the students’ background and personal characteristics and elements reflecting the context of their schools, there were still significant gender differences in Australia. Comparisons are made with similar studies using data from the Second International Science Study.