This paper reports a two-year longitudinal study of the effects of cooperative learning on science attainment, attitudes towards science, and social connectedness during transition from primary to high school. A previous project on cooperative learning in primary schools observed gains in science understanding and in social aspects of school life. This project followed 204 children involved in the previous project and 440 comparison children who were not as they undertook transition from 24 primary schools to 16 high schools. Cognitive, affective, and social gains observed in the original project survived transition. The implications improving the effectiveness of school transition by using cooperative learning initiatives are explored. Possibilities for future research and the implications for practice and policy are discussed.