The article deals with monitoring the use of financial resources from EU Structural Funds to support innovative activities in the Slovak Republic, the Czech Republic, Poland and Hungary not only in the present, but also in the previous programming period (2000-2006). It describes the areas to which financial resources from the EU Structural Funds flow. It also indicates the operational programmes and their priorities that deal with the promotion of innovation and innovative activities in the countries, the total amount of financial resources allocated to support those activities, the numbers of proposed projects and numbers of projects approved for implementation. The actual use of financial resources from the EU Structural Funds and the State Budget is also described in each section. The article includes a description of which areas are the most supported by the EU Structural Funds in the current programming period (2007-2013) and a description of the support to the area of "Research, technological development, innovation and entrepreneurship".