European innovation scoreboard is used to monitor and compare the innovation performance of European countries, according to which was the Slovak Republic, together with two other V4 countries, i.e. Hungary and Poland, at the time of last available data from this area, classified into the last, fourth group of countries named “catching-up countries”. These countries were characterized by the lack of innovation activity, which was well below the EU 27 average. From the V4 countries, Czech Republic achieved the best results, belongs to “moderate innovators” and is the most close to the European average. At a present time all four countries are included in a group of moderate innovators.The innovation performance of whole country is particularly influenced by innovation activities of enterprises operating in this country. For this reason, the article deals with the detailed analysis of innovative activity of enterprises by their size and sector of their operation in Czech and Slovak Republic, and also deals with the cooperation of enterprises in these activities in terms of the type of partner and the countries of their interaction.