A case study of the magnet school program in an anonymous midwestern United States city provides insights on the types of organizational and political changes that result from this form of school desegregation. Organizationally, the normal life of school systems depends upon a delicate balance of two sets of contradictory elements: individual school and teacher autonomy, on the one hand, and the larger administrative structure of the entire system, on the other. The use of magnet schools to achieve desegregation changes the balance of authority by: (1) formalizing the existence of variation in school practice; (2) tightening the linkage between the school system and individual schools; and (3) giving increased power in the organization to parents as clients. In addition to these organizational changes, by contradicting the principle of equivalent education and facilities among different schools, the magnet system exacerbates political conflict, particularly with regard to competition for resources between minority and privileged goups. Elitism becomes a significant problem when white or wealthier students are disproportionately drawn to magnet schools. Given the changes described above, it is understandable that the magnet system has provoked resistance from teacher unions, office and instructional staff, parents and, at different times, the black and white communities. (Author/GC)