The rapid expansion of school choice is restructuring public education in the United States. This study examines associations between charter and magnet school enrollment, White-Black and White-Hispanic segregation, and test score gaps at the district level from 2009 to 2015 in third to eighth grade using the Stanford Education Data Archive and the U.S. Department of Education's Common Core of Data. Robust findings indicate that higher charter school enrollment is associated with larger White-Black test score gaps and this effect is mediated by White-Black segregation. There is also evidence that magnet school enrollment is associated with White-Hispanic test score gaps. Overall, this study suggests that the expansion of school choice may have negative implications for structural education equity.