This paper deals with allocation of financial resources from selected operational programmes among Czech regions and assess whether a regional innovation paradox occurs in the Czech Republic. Regional innovation paradox expresses a state when some regions with lower innovation performance and higher investment needs exist but at the same time these regions are not able to gain the offered resources. The article examines the relationship between amount of obtained resources and selected characteristics of regions through correlation and cluster analysis. The attention is focused on Operational programme Enterprise and Innovations and Operational programme Research and Development for Innovations. The analyses confirmed the existence of the regional innovation paradox in the Czech Republic. The paradox is apparent especially if the amount of subsidies is compared to the total regional gross domestic product. The paradox is in higher degree apparent at OP Research and Development for Innovations than OP Enterprise and Innovations.