This paper uses pupil responses to the PISA study in 2000 for all EU countries. Using indicators of the pupil intakes to schools and their outcomes it computes segregation indices for 15 countries, and then tries to explain the resulting patterns in terms of the characteristics of national school systems. Segregation by sex in each country is explicable by its provision of single-sex schools, religious schools, and the use of academic selection in allocating school places. Segregation by outcome is largely explicable by the use of academic (and other forms of) selection. Segregation by parental occupation or country of birth is lower in countries allocating places at school through elements of choice or with relatively little governmental control of schools rather than use of rigid catchment areas or selection. In all countries there are small gaps between the performance of boys and girls in reading, in favour of girls. This gap is generally smaller in countries with the highest overall scores. Overall, the Scandinavian countries of Sweden, Finland and Denmark show less segregation on all indicators, while Germany, Greece and Belgium show the most. The UK has below average segregation in terms of all indicators except sex, despite a commonly held but unfounded view that segregation in the UK is among the worst in the world.