The purpose of this study is to highlight the important aspects on the creation of a criminal justice section inside prisons, as well as the creation of minimum requirements for jail and detention settings and a uniform set of rights for all EU inmates. The Council of Europe believes that efforts should be taken to improve mutual trust and to more effectively implement the concept of mutual recognition in custody, as stated in the Stockholm Program, which calls for the Council to address detention and related concerns. Among the instruments of mutual recognition of terms of incarceration that may be affected we mention the European Arrest Warrant issued by the Council, the transfer of prisoners, the mutual recognition of alternative sanctions and judicial proceedings, and the European supervision order. Following the analysis and empirical research, the paper summarizes that without mutual trust in detention, the European Union's mutual recognition instruments affecting detention will not work properly, as one Member State is unwilling to recognize and implement a decision taken by the authorities of another Member State. Without greater efforts to improve detention conditions and promote alternatives to detention, it may be difficult to develop closer judicial cooperation between Member States.