The European Union gives universities an important place to participate in research and development in the country. The basic research and teaching process of higher education institutions is gradually becoming more and more scientific, and the importance of science and research is growing. Th e growing importance of R&D for universities also increases the importance of public support in this area. Slovakia was eligible for support from the structural funds by joining the EU. In the period 2007 - 2013, universities have had the highest increase in science and research spending due to the use of these resources. However, it is a question of the extent to which this form of public support has contributed to the field of research and development of higher education institutions and whether there has been a real increase in their research and development activities. We examine the effectiveness of the support granted to public universities from the European Union Structural Funds on the basis of measurable indicators of granted projects and the impact of outputs on their scientific research potential in the regions of Slovakia. The results of the analysis highlighted the high level of public support for university infrastructure projects at the expense of support with a focus on intellectual property creation and patents. The discussion is focused on whether the funds allocated in this way were effective in relation to the objectives of the Operational Program Research and Development 2007 - 2013 and thus contributed to an increase of scientific and research potential at higher education institutions in the regions in Slovakia.
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