In the wake of the post-pandemic era, the reuse of existing data for scientific research has emerged as a critical policy focus. This thesis delves into the European Commission’s 2022 proposal, aimed at establishing a sector-specific regulation governing the secondary use of health data within the European Union and its interplay with the General Data Protection Regulation (‘GDPR’). This ambitious initiative seeks to harness the potential of novel technologies while streamlining administrative processes. However, the pursuit of efficiency often implicates compromises in privacy and fosters power imbalances and therefore does not result in an alignment with the GDPR. This research underscores the importance of aligning the proposed regulations with the GDPR’s principles and safeguards, particularly concerning the handling of sensitive personal health data. The GDPR mandates stringent rules to protect health data due to the profound economic, psychological, and societal harms that unauthorized access or sharing may pose. By illuminating these ethical quandaries, this thesis aims to advocate for a balanced approach that upholds both efficiency and privacy while leveraging emerging technologies for scientific progress within the EU.