One of the most frequently studied factors relating to the rise of educational inequalities is the selectivity of the education system. Selectivity often gives rise to inequalities in educational opportunities. The Czech Republic exhibits large inequalities in educational achievement and relatively steep socio-economic gradients in all international comparative studies. The combination of high educational inequalities, a strong relationship with socioeconomic background, and high selectivity of the education system is regarded by Czech society as fairly acceptable. Moreover, lowering education inequalities is not a critical issue for Czech education policy-makers. As a result, some of the currently adopted measures of education policy threaten to strengthen the inequalities to an even higher extent. In this study, the authors aim to bring more empirical evidence to the issue of educational inequalities with attention to the structure of the system based on the data from international large-scale surveys. The authors pose two sets of questions. The first set is concerned with the extent to which tracking produces these inequalities: What is the magnitude of education inequalities at different levels of the education system? What are the differences among students in different types of schools? The second set of questions is concerned with regional inequalities in educational achievement, and how these may contribute to overall levels of inequality. To what extent do results differ among regions for students in their last year of lower secondary school? Do characteristics of the populations living in these regions explain some of the variation? (Contains 2 tables and 3 figures.)