EUROCAT is an established European network of population-based registries for the epidemiologic surveillance of congenital anomaly (CAs). EUROlinkCAT will use the EUROCAT infrastructure to support 21 EUROCAT registries in 13 European countries to link their CA data to mortality, hospital discharge, prescription and educational databases. Each registry will send standard aggregate tables and analysis results to a Central Results Repository (CRR) thus respecting data security issues surrounding sensitive data. The CRR will contain standardised summary data and analyses on an estimated 200,000 children with a CA born from 1995 to 2014 up to age 10, enabling hypotheses on their health and education to be investigated at an EU level. This enhanced information will allow optimisation of personalised care and treatment decisions for children with rare CAs.