The aims of the study were to examine changes in school segregation across different types of municipalities between 1998 and 2011 in Sweden, and to explore the extent to which these changes are the consequences of school choice. Multilevel models were applied to register data using a counterfactual approach. The results showed that school segregation with respect to migration background and educational achievement had increased over time, while social segregation remained rather constant. The degree of school segregation varied largely across different municipality types, and it was concluded that school choice was a determinant of school segregation. The findings have strong policy implications and are discussed in relation to the recent educational reforms in Sweden.