The development of an Area of Freedom, Security and Justice under the Third Pillar of the European Union has significantly increased the extent to which EU legal acts might be the subject of applications to the European Court of Human Rights in Strasbourg. In this article, the author argues that while the European Court of Justice in Luxembourg has historically taken care to ensure legal harmony in an otherwise uncertain legal context, some recent proposals under the Third Pillar, such as the draft framework decision on procedural guarantees, have been less clear about the relationship between EU legal acts and the European Convention on Human Rights. Furthermore, the author argues that while the Strasbourg court’s judgments in Matthews and Bosphorus helped clarify the scope of its jurisdiction with regard to EU legal acts, the Luxembourg court’s judgment in Pupino would seem to reinforce the discretion left to national authorities in applying Third Pillar legal acts and thus also the scope of the Strasbourg court’s jurisdiction in cases concerning their implementation.