Secondary use of personal data is particularly challenging for research, especially in paediatrics. The new EU General Data Protection Regulation (GDPR) enables a new legal framework for the data protection and personal data processing. This article analyses the GDPR provisions with the aim to verify if paediatric peculiarities are taken into account in the new framework and if GDPR provides adequate and clear rules to favour the secondary use of paediatric data for research purpose in international contexts. The analysis points out the lack of specific provisions covering paediatric peculiarities in the rules introduced by the GDPR, especially in the case of secondary use of data in international research projects. It concludes underlying the importance to develop new overall governance of personal data processing for health research in order to reduce the risk of infringements of fundamental and child’ rights. The need of further safeguards and tools for the standardisation of practices is also emphasised.