The university is Iosing its position as an autonomous institution for research and education. Intemal changes at universities forced by external factors are contested by the academic milieu of the most prestigious institutions. The author suggests using the autonomy of Polish universities as a tool for innovative self-organization. He stresses the successes of both inter-departmental and interuniversity interdisciplinary and transdisciplinary initiatives undertaken by the Polish academic milieu itself (e.g. College of Inter-Faculty Individual Studies in the Humanities, College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, 'Artes Liberales' Academy). In his opinion, intemal self-reorganization of autonomous universities in Poland is the only way of introducing innovations at the best of them. The revival of mutual trust between students and masters is the 'conditio sine qua non' of successful transformation.