Using panel data that track individual students from year to year, we examine the effects of charter schools in North Carolina on racial segregation and black-white test score gaps. We find that North Carolina's system of charter schools has increased the racial isolation of both black and white students, and has widened the achievement gap. Moreover, the relatively large negative effects of charter schools on the achievement of black students is driven by students who transfer into charter schools that are more racially isolated than the schools they have left. Our analysis of charter school choices suggests that asymmetric preferences of black and white charter school students (and their families) for schools of different racial compositions help to explain why there are so few racially balanced charter schools. © 2006 by the Association for Public Policy Analysis and Management.