AbstractIntroductionThe paradigm shift to a knowledge‐based economy has incremented the use of personal information applied to health‐related activities, such as biomedical research, innovation, and commercial initiatives. The convergence of science, technology, communication and data technologies has given rise to the application of big data to health; for example through eHealth, human databases and biobanks.MethodsIn light of these changes, we enquire about the value of personal data and its appropriate use. In order to illustrate the complex ground on which big data applied to health develops, we analyse the current situation of the European Union and two cases: the Catalan VISC+/PADRIS and the UK Biobank, as perspectives.Discussion and conclusionsPersonal health‐related data in the context of the European Union is being increasingly used for big data projects under diverse schemes. There, public and private sectors participate distinctively or jointly, pursuing very different goals which may conflict with individual rights, notably privacy.Given that, this paper advocates for stopping the unjustified accumulation and commercialisation of personal data, protecting the interests of citizens and building appropriate frameworks to govern big data projects for health. A core tool for achieving such goals is to develop consent mechanisms which allow truly informed but adaptable consent, conjugated with the engagement of donors, participants and society.