The thesis Difficulties of the EU - Cohesion Policy Implementation System in the Czech Republic in the Programming period 2007-2013 deals with application of the theories of the European integration on two case studies. In the first part of the thesis the general history of the EU - structural policy is described. The second part is dedicated to the history of the structural policy in the Czech Republic. The third part is concerned with the theoretical definition of the topic and leads to a definition of the hypothesis and the research method. The main theoretical approach for the case studies is the multi-level governance theory, which describes multi-level sharing of authority among different types of actors. None of those actors has a power to define final version of the given policy. The case studies, which in detail examine the development and the efficiency of the implementation system of structural policy in Czech Republic, prove that this environment can cause the coordination dilemma connected with overuse of the free-riding tactics and high transaction costs. The combination of those elements leads to highly rigid system of implementation.