Many studies show that one of the most important factors related to delivering equity in education is the design of education system, its differentiation, and the age at the time of the first selection. Most studies agree that tracking has no impact on overall achievement but contributes to inequality. In the Czech Republic tracking is very extensive and starts in primary school where, beside the mainstream schools, some students attend schools with extended curricula, while others attend special schools with reduced curricula. In all comparative studies the Czech Republic shows a strong relationship between student achievement and socioeconomic background and large differences in achievement and study conditions between different tracks. The Czech Republic is also repeatedly criticized for disadvantaging Roma children by diverting them to a disproportionally large extent to special schools. This paper explores the differences in achievement, educational experiences and aspirations between Roma students and students from the majority population and between Roma students educated in different settings. The analysis is based on Czech data from PISA 2009, where schools in areas with high proportions of Roma citizens were oversampled so that the mainstream schools, schools with majority of Roma students and special schools were equally represented.