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During the last two decades Estonian higher education system has undergone great changes. It has been transformed from the rigid Soviet system to a modern European system that is guided by the Bologna process. Graduate (PhD) education system was rebuilt from scratch. These changes have had major implications and only recently Estonian graduate education system started to reach to these quality levels that are necessary to support the knowledge-based society. In this paper we will focus on one of the measures to increase quality of graduate education, namely graduate schools. We will describe Estonian Graduate School in Information and Communication Technologies, analyze the impact of this school to our graduate education and explain the problems and shortcomings.