Abstract. The paper deals with the transformation of a transition society (using Estonia as an example) into knowledge-based society, and developing doctoral studies as its key element. Doctoral studies gained impetus from the second half of the 1990s and in conformity with the Bologna process, principles applied in European universities infrastructure, doctoral study programmes and a new paradigm of supervision are developed. To improve cooperation of numerous new supervisors and doctoral students it is necessary to rely more on the international experience in organising modern research-based studies, applying supervision methods and research collaboration of different sectors of society. The core problems discussed in the paper include the institutional organisation of doctoral studies, cooperation of students and supervisors, and the collaboration of academia and industry in training and using top level specialists.