Collaboration between universities, business and government is important in creating innovation, but often they face barriers which block the successful cooperation among institutional spheres. To improve and strengthen collaboration and overcome existing barriers were created hybrid organizations (like university science parks, research centres or incubators) to address innovation blockages. With the growing popularity of this tool among regional policy makers, there is a need to specify their roles and functions in regional innovation systems. The main goal of our paper is to examine the contribution of university science parks and research centres in Slovakia, which were built thanks to financial support from European Structural and Investment Funds (ESIF). University science parks (USPs) and research centres (RCs) are tools for connecting the university, industry and government sector in a Triple helix framework. They create a suitable space for generating innovation with existing resources at universities, research institutes, research departments of companies and governments, and improve them through mutual interactions. We applied the method of quantitative research – an online questionnaire survey complemented with interviews, which we used to collect basic data on all science parks in Slovakia. The key question in the article is whether research infrastructures represent effective investment with long-term sustainability. We evaluated the current functioning of the parks in terms of fulfilling the functions that contribute to innovation creation, because quality and modern infrastructure is a prerequisite for the implementation of research, the results of which have a high development and innovation potential. We found that the research infrastructure doesn’t perform the required functions, which were declared during their creation. The main barriers to development include insufficient funding for research, technological infrastructure and long-term financing of professional staff. Unclear conditions for the continued operation of parks and uncertain position of government support shows that these investment projects financed by the European Funds are not independently viable after the end of the sustainability period.