The article deals with the issue of structural and cohesion funding by the European Union in Poland. Although all funds for the first programming period 2004–6 were allocated, the process did not occur without problems. Therefore, in our paper we point to the weaknesses of the system and some of the crucial barriers that hindered efficient fund allocation: faulty institutional and legal framework, bureaucracy, corruption and personnel deficits. We base our findings on research of interviews carried out in four regions of Poland. Referring to Niklas Luhmann’s theory of autopoietic system, we sketch an image of an unevenly differentiated political system, in which administration and politics prevail over the underdeveloped and weak public, incapable of counteracting trends of politicization and expanded bureaucracy. By showing evolution and reproduction of the system, we relate to its deficits and their importance to future use of the flow of EU funds.