In the Federfarma case (2005), the Italian Consiglio di Stato refused to request the European Court of Justice to give a preliminary ruling, stating that the fulfilment of EC obligations would have implied the violation of a fundamental constitutional right. TheFederfarma decision is noteworthy for many oddities, but its main reason of interest lies in the conception of fundamental rights which it expresses: to put it shortly, fundamental rights as “freedom of the State”. This conception is relatively new, but it is not unusual, and it is crucial for the judicial management of a multilevel system of governance. This Article argues that the discourse on fundamental rights underpins a marked flexibility and indeterminacy in the relations between autonomous jurisdictions; however, in the long term, case-sensitive application of fundamental rights may increase the loss of legal certainty and accountability. Depending on how they are understood and applied, fundamental rights can produce an effect of mutual delegitimisation between the orders in conflict, of uncertainty of law and political overexposure of judicial power. The dynamic of legal and institutional pluralism demands the creation of procedural channels that work as tools of dialogue. Rights alone are not enough in a multilevel system.