The article examines harmonization of higher education as an prerequisite of improvement of study quality in Lithuania. It overviews the development of higher education and criteria of university and higher non-university study programmes. An assumption is made that higher university and higher non-university studies are poorly harmonized and the strategy for realization of studies is lacking relevant coherence. Unification of assessment criteria shows lack of harmonization in and between non-university and university studies as well as the problem of realization of the mission of components of a binary higher education system. (Contains 1 figure and 2 footnotes.)