The purpose of this paper is to present two basic ways in which a path has been laid for EU citizens to directly participate in decision-making on issues related to the Union, and to analyse the main obstacles for them to functioning. The direct participation criterion removed from our attention those forms of citizen engagement that rely on intermediaries who are either elected national or European representatives, or are embodied in civil society organisations. The idea of participation should have covered two fundamental instruments that directly relate to citizens: national referenda on European issues and the European Citizens’ Initiative. Our analysis shows that there are several obstacles in the construction of the Union which have a significant effect on any reference to the directly expressed will of the people. The basis of this great number of problems is certainly the specific multi-layered political arena of the Union, which, on one hand, weakens any national referendum in terms of its supranational significance, and, on the other hand, imposes on citizens, through the European Citizens’ Initiative, high requirements to adapt to the logic of supranational mechanisms. When considering the complaints that are usually directed at the direct decision-making of citizens, the idea of establishing a direct link between the Union and the citizens of particular Members States still has a long path of development before it.