EU membership affects state institutions in two key ways. First, governments must organize themselves to deal with the EU and participate in its decision-making processes. Second, participation in the EU’s multilevel system of decision making affects the balance of power among state institutions and the relationship between them, strengthening some at the expense of others. In some cases, EU membership might even require the creation of entirely new government institutions or structures. In this chapter, we examine how European integration has affected state institutions in the Czech Republic and how they have adapted to the requirements of EU membership, focusing on the government and national administration, the parliament, and the judicial system. We also examine the role of the EU in the creation of new structures for regional self-government in the Czech Republic.