Transition of a country’s economy to an innovative way of development is not possible without forming a global competitive innovation system. The role of innovation is also important in defining the concept of national competitiveness as the key country's ability to innovate. Innovation activity in SR, compared with the ones in economies of other European countries, is lower and innovation do not yield an expected positive outcome in the form of increased competitiveness of Slovak enterprises. The Slovak Republic has a developed industrial base, which can help to transform the country into a knowledge economy, provided that innovations will be largely used throughout the entire structure of economic activities.