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The aim of the paper is to provide an overview of the development of Czech innovation policy which started to get its shape in the first years of the 21st century. The article traces its origins to a number of interlinked factors - the introduction of European regional policy in the Czech Republic, the increased inflow of foreign direct investment into R&D-intensive sectors and also the devolution of power to Czech regions that were established in 2001 and gave a new, regional dimension to research and innovation policy. It pays particular attention to the process through which the regionally-based innovation policy advocated by the European Union (EU) has been translated and adapted in the context of a new EU member state. As an illustration of the efforts at the regional level to make a better use of the potential of R&D and innovation in the regional development, a case study of a regional innovation strategy of the City of Prague is analysed. The City of Prague was selected for a critical analysis of an innovation system and innovation policy due to the fact that it is a region with significant but until now not fully exploited innovation potential and, in addition, its first innovation strategy has been recently adopted. The innovation strategy is closely scrutinized and the process of its elaboration is critically examined within the European and especially national context. The authors demonstrate that there is a lot of conceptual ambiguity and confusion associated with the process of transferring the experiences of Western European regions to the Czech Republic. The authors believe that at least some of their observations and analysis of weaknesses of the process through which the regional innovation strategy (RIS) has been carried out will have relevance for other Czech regions and even for other regions in the new EU member states. [ABSTRACT FROM AUTHOR]