Soviet higher education had a distinctive institutional landscape. It combined two institutional types in a uniform model that embedded higher education in the national economy. This paper focuses on the post-Soviet system-level changes in the institutional landscape in all 15 countries of the former USSR. It shows that over last three decades the Soviet two-type institutional model evolved into a three-type model, with the specialized university as a new institutional type. Highlighting the instruments of horizontal and vertical differentiation for each country, the paper explains how structural reforms and market forces led to the rise of the university/multiversity form of institution, and the strengthening of vertical stratification at system level. The comparative analysis shows that there have been different patterns of transformation in the 15 countries, shaped by unique combinations of structural reforms and marketization policies, with certain countries having made more distinctive steps away from the Soviet institutional model. There are now 15 formally different systems of higher education which poses further questions for comparative analysis.