This article summarizes current issues regarding preparation and implementation of EU projects. Cohesion policy and regional policy as a main part of cohesion policy are the most important policies of European Union. This could be view also from the volume of financial resources allocated for these policies. One of the main current research issues is analysing efficiency and effectiveness of these funds. Examining the effectiveness of funds we can see a number of shortcomings, from which the most significant are deadweight loss, lack of application of the principles of partnership, administrative burden focused on expenses and not results, the low multiplier effects and little focus on the priorities of promoting competitiveness. The author have analysed several of them directly in the case study of Banská Bystrica region.