Recent EU initiatives and legislation considerably increases public access to clinical trials data (CTD). These are generally much welcomed developments for the enhancement of science, trust and open innovation. However, they also raise many questions and concerns. Many of these emerge at the interface of CTD transparency with other areas of evolving EU law concerning the protection of trades secrets, IPRs, and privacy. This paper focuses on the privacy issues by analyzing the interrelation between the transparency developments and the EU’s new General Data Protection Regulation 2016/679 (GDPR). More specifically, this paper examines (1) the genesis of the EU transparency regulations, including the incidents, developments and policy concerns that have shaped them; (2) the features and implications of the GDPR in the context of clinical trials; and (3) the practical difficulties and risks for tensions between the GDPR and the policy goals of CTD transparency and open innovation. Ultimately, we stress that such factors must be carefully considered and addressed to reap the full benefits of CTD transparency.