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This paper analyses impacts of the Structural Funds implementation on fostering Research Technological Development Innovation (RTDI) in Slovakia. It explores absorption of the RTDI investments from the the Structural Funds in different types of Slovak regions and analyses it via in-depth interviews with the experts on RTDI policies and professionals involved in implementation of the Structural Funds in Slovakia. Concluding section summarises findings from the statistical data and interviews, and discusses policy options for implementation of the Structural Funds in planning period of 2007 - 2013.