The more science and mathematics subjects that pupils in pre-university education include in their final examination package, the more future academic routes are available to them. Equality of educational opportunity is thus threatened when groups of pupils, distinguished by sex and family background but otherwise of equal capacities and achievement, are found to differ in their choices. This proposition is examined using data from a large Dutch cohort. Multilevel analyses show that the choice of science and mathematics subjects by girls is influenced by their family background while the choice by boys is not. The influence of various pupil and family variables on the subject selection process is explored via path analyses. The results confirm the importance of viewing subject choice as a chronological process that progresses differently for boys and girls. (Contains 4 tables and 3 figures.)