The article addresses the role of the European Union and the European Court of Human Rights in resolving the issue of Roma segregation in the education system, which the author considers an ongoing and serious social problem. The introduction defines segregation as the uneven distribution and concentration of social groups in space, leading to their isolation. The author draws on current statistical data showing that the problem of segregation in education is not improving over time, and emphasizes the negative impacts of segregation on educational outcomes, child development, and the overall quality of the education system. The article further analyzes the legal framework prohibiting segregation in the EU and national laws with particular focus on the situation of Czechia, Slovakia and Hungary. It provides a detailed examination of the conclusions from the case law of the European Court of Human Rights and the Czech and Slovak Supreme Courts on the issue of segregation. It analyses the question whether there is a need for a more active approach of the EU in this area.