The paper deals with the issue of managing structural funds in Zlínský and Trenčiansky Regions on the Czech-Slovakian border with the focus on success of targeting funds to local entrepreneurs, especially small and medium ones. An expansive dataset was used to evaluate the process and to compare it with relative advancement of the regions in terms of their economic and social development as described by the development index created by the authors and based on the regional policy of Zlínský Region. The results brought forward in this paper are somewhat ambiguous in terms of usefulness of European funding at the most disadvantaged regions, especially Trenčiansky. On the other hand, Zlínský Region, being more successful in supporting the disadvantaged areas, is still slightly less efficient in supporting smaller organizational forms of entrepreneurship. The differences between these two regions are growing even further due to significantly different amount of funds available to them. JEL Classification: H25, L53, O22, R58