With the Treaty of Lisbon agencies were officially recognized as part of the institutional design of the European Union while the Charter of Fundamental Rights of the EU became binding on the EU and its member states. In order to include fundamental rights concerns into the everyday practice of EU governance, the Fundamental Rights Agency (FRA) was established in 2007. Since then, the FRA has signed a number of cooperation agreements with the other agencies of the Area of Freedom Security and Justice (AFSJ), such as Frontex, but also EASO, Europol and Eurojust. How are these cooperation agreements working? What has been the impact of FRA on mainstreaming human rights in the AFSJ? These questions will be addressed by analysing specifically the relationship between FRA and Frontex though semi-structured and expert interviews, and by examining how human rights have been framed since the signing of the cooperation agreement in 2010.