Swedish education system has become uniquely market-driven with a high degree of choice and student mobility after the school reforms in the past decades. Coupled with the societal changes, Swedish schools have become increasingly segregated, manifested by the increasing gaps in educational resources and teaching quality, and staffing challenges along social and spatial lines and across school types. This has led the compensatory function of schools for individual life prospects and social cohesion to deteriorate, resulting in a complex interplay between family, school, region, and system-level features, which has yet to be adequately studied. The research program SIS aims to investigate the mechanisms and long-term consequences of segregation in all stages of schooling and the transition to the labour market. Nine researchers united from education, sociology, child and youth studies and human geography disciplines will dedicate their expertise in four under-researched areas: social sorting of student over school stages and spaces, teacher sorting and mobility, segregation’s long-term consequences, qualitative experiences and social dynamics in educational choices and school segregation. Relying on a mixed-methods approach, and register and interview data, the project aims to contribute knowledge regarding school segregation, provide evidence-based recommendations to counteract school and societal segregation, in turn, enhance social sustainability and integration in Sweden.