The Swiss cantonal education systems account for the structural organisation of lower-secondary education (streamed, cooperative or integrated models). We examined whether structural cantonal variations affect students’ transition to upper-secondary education. Analyses drew on data from the TREE study. Multilevel logistic regression analyses indicated that students in cantons with a cooperative or integrated model had, by trend, a higher chance of gaining access to upper-secondary education. The effect was confounded with the language regions.