The master thesis deals with innovation systems in the Slovak Republic. In the first part we theoretical basis on this matter, as the characterization of innovation, its competitive advantage, classification of innovation and innovation system consisting of national, regional, and sectoral innovation system. Conclusion the theoretical part of master thesis will be dedicated to current instruments for support of innovation in the Slovak Republic and in selected countries . The practical part of master thesis is dedicated to the knowledge and use of selected instruments of the innovation system. Analysis of knowledge and use of these Instruments is carried out throught a questionnaire survey. The results point to the fact that company mostly know the selected instruments for support innovation in relation to their use. Discussion of the issue which has been addressed deals with the possibilities of optimization, removing barriers and measures that would significantly improve the use of these instruments for support of innovation in the Slovak Republic.