This paper explores some key discrepancies between two sets of normative requirements applicable to the research use of personal data and human biological materials: (a) the data protection regime which follows the application of the European Union General Data Protection Regulation (GDPR), and (b) the Declaration of Helsinki, CIOMS guidelines and other research ethics regulations. One source of this controversy is that the GDPR requires consent to process personal data to be clear, concise, specific and granular, freely given and revocable and therefore has challenged the concept of ‘broad consent’, which has been widely applied in the context of biobanking. Another source of controversy is the interplay between regulations of research ethics and protection of personal data related to the secondary use of personal data and biological materials. In this case, the GDPR ‘research condition’ provides an alternative to re-consent for the use of previously collected personal data and biological materials. Although the mentioned controversies have been raised in the legal literature, they have not been explicitly addressed from the research ethics perspective. Should consent be regarded as a priority legal basis for personal data processing in health data research? Can broad consent still be a suitable legal ground for biobanking? What should be the role of research ethics provisions that differ from the GDPR standards, and what should be the role and function of research ethics committees in the changing environment of health data research? These are the ongoing controversies to be explored in the paper.