The text deals with the cross-border co-operation of universities as a possible new research topic in border studies. We identified two important associations of universities operating in border areas in the EU core and two associations gathering universities from Czech, Polish and Slovak areas. Then we tried to identify the areas in which these universities co-operate. It turned out that the principal difference is in significantly higher level of functional cross-border integration of the universities in the EU core, which is evidenced mainly by higher number of joint study programmes. We believe that the topic is promising and deserves much higher attention, as it points at new and not really exploited cross-border integration potential for universities located in border areas of V4 countries