Arguably, big data, data processing with advanced ICT solutions and data sharing were accelerated during the end of the 2010s, also fuelled by the COVID-19 pandemic. This latter can be reasonably considered a booster in health care for data-driven digital solutions and regulations, which led to issues concerning both primary and secondary use of digital (electronic) health data. There is an ongoing and comprehensive regulatory effort within the European Union to address the evoked challenges. Regarding the healthcare sector, the European Health Data Space Regulation can be considered a flagship legislation. The main ambition of the European Commission is, on the one hand, to create a common space where natural persons can easily control their electronic health data and, on the other hand, to make it possible for researchers, innovators and policymakers to use these health data sets for common societal purposes in a trusted and secure way based on a specific cross-border digital infrastructure. A European Union project, the Joint Action Towards the European Health Data Space (TEHDAS) has been initiated to support the establishment of the EHDS as regards the secondary use of data. Our analysis identified two important topics: legislative barriers to the secondary use of health data and challenges for citizens’ empowerment, including data altruism. The legal complexity of the ongoing strategic legislative initiatives within the EU poses several challenges for future application. Firstly, there can be a terminological issue based on the lack of a common definition of secondary use of data. Secondly, the regulation of the Member States adjusted to their national health and data utilisation systems can be diverse. Both of these may hinder the desired EU-level harmonisation regarding data-sharing. In this context, the division of regulatory competencies related to health care and the chosen legal basis can be decisive. Overall, the EHDS might be a regulation that can challenge the current legal paradigm of competence distribution among the EU and the Member States regarding digital transition, including data usage in health care. As for the citizens’ empowerment, the goal of an EU-wide ecosystem of health data utilisation requires individuals who are aware of the economic value of their health data and, via practising altruism, want to use these data also for the common good. Specific provisions of the EHDS, such as the right to data portability or the option for opt-out, are definitely for the empowerment of citizens. But, these can also reduce the potential health care-related benefits of data utilisation at both, individual and population level. Altogether, a concert of requirements should be fulfilled for meaningful citizens’ participation, engagement, and practice of data altruism, supported by the complex interplay of the relevant regulations.