The European Union Animal Health Law lays down a robust legal framework for the management of listed infectious disease risk in animals under human care. It also builds on extensive experience (primarily gained from the Balai Directive) to provide tailored mechanisms and procedures (e.g. through the Confined Establishment status) that ensure adequate prevention, mitigation and risk management of listed infectious diseases in non-domestic animal species housed in facilities such as zoos or other conservation institutions. This tailoring recognizes the unique requirements and constraints of keeping and breeding wildlife species for conservation purposes, and the capabilities of the professionals tasked with their care, and of the institutions that house them to ensure high standards of biosecurity, disease surveillance and control measures. The European Association of Zoos and Aquaria (www.eaza.net) and the European Association of Zoo and Wildlife Veterinarians (www.eazwv.org) have partnered with the European Association of State Veterinary Officers (a section of the Federation of Veterinarians of Europe, www.easvo.fve.org) to produce this guidance document that distills and compiles the pieces of legislation in the AHL relevant for Confined Establishments. Guidance is provided on the processes and procedures that can be implemented to comply with the AHL by leveraging best practices in zoological medicine and management. We hope this guidance document will be of assistance to a range of stakeholders, including zoo animal managers, veterinary practitioners providing healthcare to non-domestic species and to official veterinarians working with zoo animal health controls.