Analysing the EU’s System of Government on the basis of the treaties establishing the Community and the Union leads to identifying five basic government functions, which are distributed in a complex system of checks and balances between the EU institutions and between the latter and member states’ institutions. Those five functions may be characterised as legislative function, which evolved over time from rule making to law making, the executive function which consists in implementing common policies, the supervisory function, consisting of judicial review and of oversight of member state’s compliance with their treaty obligations, the function of direction, consisting of policy guidance and programming, and an organic function consisting in institutional development. The new wording of the relevant treaty clauses by the Lisbon treaty clarifies the nature and distribution of these five functions and thus enable us to understand how separation of powers is organised in the EU.