Many studies show that one of the most important factors related to delivering equity in education is the design of education system, its differentiation options, and the age of the children at the time of the first selection of a school type (OECD 2007). In a system in which early self-selection is constrained there is less educational inequality than in a system where consequential decisions about the educational career are taken at a very young age (Erikson and Jonsson 1996). Early selection leads to distribution of children according to their socio-economic background. In early selection parents are more influential. Educated parents value education and they can give their children advice on strategies that are not likely to constrain later choices. Lower-class children experience less encouragement from their family. Early assignment to low ability tracks is demotivating. The research shows that students when assigned to low ability classrooms show slower progression than in mixed-ability settings (Hutchmaker, Cochrane 2001, Slavin 1990, Harlen and Malcolm 1999). Czech educational system is very selective. Many children make their first choices at primary level when they apply for schools/classrooms with extended curriculum; next choice is made at the age of 11, the age of transition to long academic tracks. In most international comparative studies of student achievement the Czech Republic exhibits a relatively strong relationship between student achievement and family background and high differences between achievement of students in individual tracks (Matějů, Straková 2005, Straková 2007). Achievement of Czech students is continuously deteriorating. At the same time the ongoing curricular reform opens space for even higher differentiation in the system. The aim of the paper is to study the level of educational inequalities in various stages of student education career (grades 4, 8 and 10) in the Czech Republic in comparison with systems without early tracking (the Nordic countries) and to explore the development of inequalities in the Czech system of primary and secondary education during the last decade. It also seeks answer to the question which groups of students are mainly affected by overall deterioration of achievement. The paper tests hypotheses that the level of educational inequalities has been increasing and that students in low ability tracks are those who suffer most from the growing differentiation of the Czech education system. The analysis was conducted on data sets from the IEA PIRLS 2001, the IEA TIMSS 1995, 1999, 2007 and the OECD PISA 2006.