Australia's continuing participation in international science studies such as the Third International Mathematics and Science Study (TIMSS) provides a useful lens through which to monitor achievement in science over time. Gender differences in science were not evident in the early years of TIMSS but appear to be growing. This article examines gender differences in science achievement in early secondary schooling in Australia using data from the TIMSS 2003 study. The aim is to explore the cultural, social, structural and institutional factors that may differentially influence science achievement, with the aim of identifying which are more important for males and for females.