The article presents a comparative analysis of the  institutional university autonomy of the following EU member states: Denmark, Lithuania, Romania, Scotland and Sweden. Today we are witnessing the restructuring of various society sectors - the economy, labor market, social and political systems, etc. It is a process at state – nation level, as well as regional and global levels. Education systems in most countries, at their turn, react to this process and engage in radical reform of higher education in order to achieve economic, social and political objectives of the society. In this emerging environment universities have to review their position in order to redefine and adapt their functions, forming an autonomous space for proper decision making and, thus, playing an innovative role in the socio-economic environment.