The Clinical Trials Regulation has opened a new era for the conduct of clinical trials in the European Union (EU). One of the main features of the Regulation is the creation of the EU portal and the EU database for clinical trials, which are intended to simplify and harmonise the submission, assessment and reporting of clinical trials. This Regulation gives the Agency the responsibility to prepare, in collaboration with the Member States and the European Commission, the functional specifications for these systems. The application of the Regulation will take place after an audit of the EU portal and the EU database has shown these systems are fully functional. This audit will be based on the functional specifications outlined in this document.