We analyze how transnational, global and international forces have interacted with Polish higher education system in the last two decades. There are some distinctive features of Polish higher education: its size (over 400 institutions, around 2 millions of students), diversity (coexistence of state and non-state sector) and strong academic self-organization (leading role of Rectors' Conference. strong disciplinary structures etc.). Our research is based on documentary analysis. qualitative studies and case-based analysis (example of Jagiellonian University). We present Polish higher education arena as a "microcosm" in which one can mirror many developments occurring at the European level, in particular transitions "divergence-convergence-emergence". As Polish educational reforms are mainly academia driven and are based on previous national experiences, we can witness rather "Polonia process" than "Bologna process". We discuss in detail the process emergence and implementation of innovations in the Jagiellonian University and mechanisms to introduce new organizational culture and quality enhancement mechanisms. We present a concept of a new research unit which is being organized at the Jagiellonian University: the interdisciplinary Centre for Research on Higher Education, aiming at integration of theory and practice of higher education management; our concept can be useful for academics, administrators and policy makers.