The European Health Data Space and biobanking in Europe: synergies, tensions and the future governance of data-driven health research

Abstract

The European Health Data Space (EHDS) represents the most ambitious attempt to date to create a common legal, technical and governance framework for the use of health data across the European Union. Its adoption creates a new infrastructure for both primary use, focusing on cross-border access to electronic health records for care, and secondary use, centred on research, innovation, public health, regulatory science and policymaking. In parallel, European biobanking has matured into a core research infrastructure supporting genomic medicine, biomarker discovery, rare disease research and precision public health. The convergence of EHDS-enabled electronic health records, BBMRI-ERIC-associated biobanks, and the 1+ Million Genomes initiative offers a plausible route towards federated, large-scale, molecularly informed health systems in Europe. This article critically examines that opportunities and challenges arising from this convergence. It argues that the EHDS and biobanking are complementary but not automatically interoperable. Biobanks provide depth: biospecimens, molecular assays, longitudinal cohorts and consented research infrastructures. The EHDS provides breadth: population-scale clinical trajectories, regulatory gateways, Health Data Access Bodies and Secure Processing Environments. The 1+ Million Genomes and Genomic Data Infrastructure initiatives provide a genomics-specific federated layer that may connect these ecosystems through standards such as GA4GH, Beacon, Phenopackets and FHIR-Genomics. However, substantial obstacles remain. These include uneven digital maturity across Member States, immature representation of biospecimen and omics metadata in clinical data models, unresolved interactions between EHDS opt-out mechanisms and biobank consent, fragmented national interpretations of the GDPR, sustainability constraints, environmental costs of petabyte-scale computing, and the risk that artificial intelligence trained on biased or incomplete datasets will reproduce health inequities. We argue that EHDS-biobank integration should not be regarded solely as a technical exercise. Rather, it represents a governance challenge involving trust, reciprocity, legal interpretation, standards development, infrastructure investment and public legitimacy. Without coordinated action, the EHDS may create a formally integrated yet substantively unequal data ecosystem. Conversely, with deliberate design and effective governance, it has the potential to provide Europe with a trustworthy, federated and clinically actionable research infrastructure.