The paper examines how and to what extent the Soviet higher education system transformed after the collapse of the USSR. It offers a research-based analysis of the external and internal factors of transformation in six post-Soviet countries: three "Slavic" states (Belarus, Russia, Ukraine), and three Baltic states (Estonia, Latvia, Lithuania). The paper characterizes a bounded number of types of organizations of higher education in each country. Using the set-theoretic multi-value qualitative comparative analysis (mvQCA), the authors identify several causal chains that led to the transformation of the Soviet comprehensive university into a 'post-Soviet research university' or 'general education organization'. This paper compares the drivers of organizational diversity in Soviet and post-Soviet education, and traces country-specific features of the organizational transformation of universities in six post-Soviet countries.