Abstract Linking records could serve as a useful tool for scientific research and as a facilitator for local policymaking. This article examines the challenges and opportunities for researchers to lawfully link routinely collected health and education data with cohort data of children when using it as a tool for scientific research in Portugal. Such linking can be lawfully conducted in Portugal if three requirements are met. First, data processing pursues a legitimate purpose, such as scientific research. Secondly, data linking complies with the legal obligations of research entities and researchers, acting as data controllers or processors, and it respects the rights of children as data subjects. Finally, data linking is based on the explicit written consent of those with parental responsibility for the child. So far, the implementation of the General Data Protection Regulation in Portugal has not facilitated record linkage. It is argued that further harmonised implementation of that Regulation across European Union and European Economic Area Member States, establishing a minimum shared denominator for record linkage in scientific research for the common good, including without explicit consent, is needed.