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Abstract Background There is a growing interest in aggregating more biomedical and patient data into large health data sets for research and public benefits. However, collecting and processing patient data raises new ethical issues regarding patient’s rights, social justice and trust in public institutions. The aim of this empirical study is to gain an in-depth understanding of the awareness of possible ethical risks and corresponding obligations among those who are involved in projects using patient data, i.e. healthcare professionals, regulators and policy makers. Methods We used a qualitative design to examine Swiss healthcare stakeholders’ experiences and perceptions of ethical challenges with regard to patient data in real-life settings where clinical registries are sponsored, created and/or used. A semi-structured interview was carried out with 22 participants (11 physicians, 7 policy-makers, 4 ethical committee members) between July 2014 and January 2015. The interviews were audio-recorded, transcribed, coded and analysed using a thematic method derived from Grounded Theory. Results All interviewees were concerned as a matter of priority with the needs of legal and operating norms for the collection and use of data, whereas less interest was shown in issues regarding patient agency, the need for reciprocity, and shared governance in the management and use of clinical registries’ patient data. This observed asymmetry highlights a possible tension between public and research interests on the one hand, and the recognition of patients’ rights and citizens’ involvement on the other. Conclusions The advocation of further health-related data sharing on the grounds of research and public interest, without due regard for the perspective of patients and donors, could run the risk of fostering distrust towards healthcare data collections. Ultimately, this could diminish the expected social benefits. However, rather than setting patient rights against public interest, new ethical approaches could strengthen both concurrently. On a normative level, this study thus provides material from which to develop further ethical reflection towards a more cooperative approach involving patients and citizens in the governance of their health-related big data.