The European Union has consistently promoted judicial cooperation between Member States, with the result that prisoners can now easily be transferred between them. Despite this, research and practice has shown that prison conditions differ significantly between Member States, and there is considerable discrepancy in their compliance with European and international standards. Significant variation between countries is also found in prison disciplinary regimes, even though they are required to act in accordance with fundamental human rights such as the principle of legality, the right to a fair trial and the prohibition of inhuman or degrading punishment. The judicial cooperation being fostered by the EU is inherently based on mutual trust and the presumption that equivalent standards are mutually respected. However, this is not the case in practice, and the EU may need to begin to measure compliance using supranational standards to maintain levels of trust. This paper argues that standards relating to prison disciplinary regimes should be reviewed to determine whether existing differences between Member States could undermine the high level of mutual trust currently existing. Judicial cooperation should be of benefit to all parties – prison disciplinary regimes that conform to international standards ensure that Member States cooperate efficiently and protect detainees from arbitrary or unlawful actions – so it is vital that it is correctly managed and monitored.