The HEREDITARY project represents an ambitious and multi-faceted approach to address the integration of complex medical data to enhance disease prevention, diagnosis, and treatment. In an era where digitalisation and machine learning promise transformative advances in healthcare, substantial legal, ethical and societal challenges persist, also due to the inherently complex, multimodal nature of health data and the regulatory frameworks governing it. HEREDITARY tackles these challenges by aiming to build a secure, interoperable infrastructure to link diverse health data sources across disease domains, centring on diseases involving the gut-brain axis – neurological diseases and gut microbiome-related disorders. The main barriers to health data integration include technical and legal complexities that limit the potential of these data sources. These variations challenge interoperability and data consistency, obstructing the development of seamless, large-scale data analysis systems. Furthermore, legal frameworks such as the EU’s GDPR introduce essential but challenging requirements, adding complexity to cross-border and multicentre collaborations. The deliverable analysis shows that the development of HEREDITARY must be guided by legal and ethical standards. The most relevant are the GDPR, cybersecurity legislation, EHDS proposal, NIS 2 Directive, and the evolving AI regulatory landscape, including the AI Act. Each of these legislation mandates robust data protection, security, and privacy measures, as well as guidelines for ethical AI deployment. HEREDITARY’s legal framework shall ensure that personal data use aligns with these requirements, fostering trusted, transparent, and ethical use of health data in clinical and research contexts. Next to these requirements, the ethical framework can help in finding the most suitable interpretative solutions in those areas where the law is imprecise, vague, or simply non-existent. Four main principles of biomedical ethics and the principles for the development of trustworthy AI systems are crucial for the HEREDITARY project. Both the legal and ethical frameworks mentioned above and further detailed in this deliverable lay the ground for the research in forthcoming deliverables of WP7 ‘Legal, Ethical and Regulatory Frameworks’.