Research on parental school choice provides strong evidence of so-called ‘white flight’ – that ethnic majority parents avoid choosing a local school if it contains large numbers of ethnic minority students. In this study, we examine such segregating choices in a formally stratified school system. Theoretically, we argue that segregating choices are less common in an educational setting where parents face stricter tracking policies. To test this argument empirically, we consider the case of German secondary schools where locally varying degrees of ability tracking coincide with a geographically unrestricted choice of secondary schools. Based on a combination of survey data from the Children of Immigrants Longitudinal Survey in Four European Countries and administrative data on the location and composition of all secondary schools in Germany, we find evidence of segregating choices among ethnic majority families in German secondary schools. Moreover, these tendencies are more pronounced in regions with less rigorous tracking systems. These findings have important policy implications, as they suggest that institutional reforms striving for greater integration may be partially offset by more segregating parental school choice. More generally, our study contributes to a better understanding of the ways in which an interplay between formal rules and discriminatory school choices often leads to persistent patterns of ethnic segregation in schools.