We describe in this article the achievements and difficulties faced during the implementation of the Inter-Unit Graduate Studies Program in Biotechnology, which has an inter-institutional structure, bringing together as it does the Universidade de São Paulo, the Instituto Butantan and the Instituto de Pesquisas Tecnológicas do Estado de São Paulo. We present and discuss the program’s structure and organization, as well as characteristics of the program’s M.S. and Ph.D. recipients. We believe that our achievements may serve as a solid basis for the implementation of other inter-institutional programs, with all their difficulties, and as a useful groundwork for the improvement of graduate studies in Brazil.