This PhD thesis deals with the protection of fundamental rights in Europe. Today, in Europe, fundamental rights are simultaneously protected at the levels of the states, of the European Union and of the European Convention on Human Rights. The purpose of this thesis is to analyze the implications of this multilevel architecture and to examine the dynamics that spring from the interaction between different human rights standards in Europe. To achieve this task, the thesis develops a “neo-federalist” narrative based on an empirical and conceptual comparison with the federal arrangement for the protection of rights of the United States of America. Rejecting both a “sovereigntist” and “sui generis” approach to the study of fundamental rights in Europe, the thesis argues that only a comparative approach can shed light on the comprehensive set of dynamics which are at play in the European multilevel architecture. The thesis identifies two recurrent challenges in the interplay between different state and transnational human rights standards – a challenge of ineffectiveness and a challenge of inconsistency. It explains that these challenges arise when transnational law operates either as a floor or as a ceiling of protection for a specific human right. In addition, the thesis maps the most important transformations taking place in the European system and assesses their impact on these challenges. To provide empirical evidence for its arguments, the thesis then considers four case studies. First, the right to due process for suspected terrorists. Second, the right to vote for non-citizens. Third, the right to strike. Fourth, the right to abortion. Since these case studies cover all the four “generations” of rights traditionally identified in constitutional scholarship (civil, political, social and “new generation” rights), the thesis aims to offer a complete analytical framework which can also be useful for future research on the protection of other fundamental rights in Europe.