BACKGROUND: The EU LeukoTreat program aims to connect, enlarge and improve existing national databases for leukodystrophies (LDs) and other genetic diseases affecting the white matter of the brain. Ethical issues have been placed high on the agenda by pairing the participating LD expert research teams with experts in medical ethics and LD patient families and associations. The overarching goal is to apply core ethics principles to specific project needs and ensure patient rights and protection in research addressing the context of these rare diseases. AIM: This paper looks at how ethical issues were identified and handled at project management level when setting up an ethics committee. METHODS: Through a work performed as a co-construction between health professionals, ethics experts, and patient representatives, we expose the major ethical issues identified. RESULTS: The committee acts as the forum for tackling specific issues tied to data sharing and patient participation: the thin line between care and research, the need for a charter establishing the commitments binding health professionals and the information items to be delivered. Ongoing feedback on the database, including delivering global results in a broad-audience format, emerged as a key recommendation. Information should be available to all patients in the partner countries developing the database and should be scaled to different patient profiles. CONCLUSION: This work led to a number of recommendations for ensuring transparency and optimizing the partnership between scientists and patients.