ABSTRACTThere are still considerable gender differences in the choice of mathematics as a subject in the second stage of secondary education. This article integrates the results of a Dutch longitudinal study into the causes of these gender differences. An outline of the elements that can influence these choices is given in a conceptual model. First of all, a description is given of the variables on which boys and girls differ. Next, the kind of changes in predictors that are coupled with shifts in subject choices are investigated. In addition, by means of multi‐level analyses the role of the school in the development of gender related mathematics achievement and the choice of mathematics is examined. The results show that schools do not differ in the development of gender specific mathematics achievement. Pre‐university education (VWO)‐schools, however, do differ in terms of the gender related choice behaviour of their pupils, especially at the moment at which the choice of subjects becomes definitive (at the end of the fourth year). Furthermore, the results show that some pre‐university education (VWO)‐schools are more meritocratic than others. In the discussion it is argued that the choice of science subjects seems to be largely determined by facets of the subject itself and the expectations of pupils and teachers