The respect of fundamental rights is one of the cornerstones of the European Union. It is a precondition of membership and it is listed among the core values of the Union. Still, as the recent controversies between the European Commission and some Member States revealed, EU law contains no effective mechanism to compel Member States to respect fundamental rights and freedoms in general. This paper presents and examines the EU architecture of fundamental rights protection. First, it demonstrates that the EU Charter of Fundamental Rights (the “EU bill of rights”) applies predominantly to EU institutions (that is, “federal” institutions); it applies to Member States only when they act as the EU’s “agents” (when they implement EU law). Although this approach may appear to be illogical, it does have its clear and legitimate reasons and it is far from unprecedented. In fact, it very much resembles the first century of the United States constitutional architecture. It is to be noted that though the EU does have the means to call Member States to account in case they violate fundamental rights, this action is a “nuclear bomb” and is hardly apt for handling human rights problems; not to mention that the application of this is almost politically unattainable. Second, it demonstrates how, in certain cases at least, the Commission “cooked from what it had” in that it used unconnected (that is, non-human-rights-related) provisions of EU law to shelter fundamental rights (e.g., the free movement principles of the internal market to protect minority rights or the prohibition of discrimination based on age to protect the independence of the judiciary). The use of the “supportive by-effects” of these economic rights is novel but not fully unprecedented. In fact, it resembles how the U.S. Congress used its commerce power to protect civil rights. Third, it argues that although the present architecture is certainly not the best of all possible worlds and the full federalization of human rights is a tempting option, the bifurcation of the “federal bill of rights” (the EU Charter of Fundamental Rights) has a solid basis and federalization is compelling only regarding those fundamental values and rights the violation of which qualifies as a “ground of divorce.” Accordingly, while the current system obviously calls for a reform, in terms of approach, this constitutional architecture has its merits in the context of what the multicolored European federation needs. On the one hand, the core of human rights protection cannot be subject to territorial variations and the violation of the nucleus of these rights cannot be justified with reference to constitutional identity. On the other hand, outside this sphere, to use the terminology of the European Court of Human Rights, European federalism demands respect for the Member States’ margin of appreciation.