The article presents the concept of throughput legitimacy for the political system of the Euro-pean Union. Throughput legitimacy was conceptualized by the American political scientist Vivien Schmidt in 2012. In Russian political science this concept was not widely used, despite its obvious practical applicability. The author aims to acquaint researchers of European integration to this concept and to show how productive its practical application for political analysis may be. The author refers to the republican and liberal traditions in European political philosophy, which are fundamental for legitimacy formulation. The methodology of the article  lies  in  the  system-based  historical  approach.  Three  features  of  the  political  system  of the  EU  are  ex-plored,  explaining  the  shift  of  the  legitimacy  balance  in  favour  of  the  republican  component.  Based  on D.Easton theory of political systems and functional theory of N.Luhmann, the author substantiates the thesis that  the  legitimacy  of  the  political  system  consists  of  three  components:  input  legitimacy,  throughput legiti-macy  and  output  legitimacy.  The  author  comes  to  the  conclusion that  in  assessing  the  legitimacy  of  the  EU political  system,  the  concept  of  throughput  legitimacy  is  the  most  adequate,  since  it  takes  into  account  the peculiar  features  of  this  system,  reflects  interrelations  within  the  system,  allows  to  estimate  the  quality  of governance and to develop appropriate recommendations.