An electronic patient record offers opportunities for digital networks between medical care providers and for the digital communication between health service providers and their patients. Patients with rare diseases benefit from a diagnosis and treatment information at an early stage and receive precise treatment on the basis of multiprofessional case management. Regarding the patient care and medical research in rare diseases, electronic patient records can help to collect all data in a structured manner and to digitally map the workflows in registration, admission, diagnosis, and treatment. This can reduce costs in our healthcare system, as diagnosis and treatment can be targeted better at the patients and unnecessary medical examinations can be reduced. In two pilot projects, first experiences with electronic patient records for patients with rare diseases were gathered. In cooperation with several medical care providers, the projects BASE-Netz and TRANSLATE-NAMSE analyzed the requirements of an electronic patient record, demonstrated the technical and legal feasibility, and evaluated the practicability for medical care providers and patients. The participating centers for rare diseases see benefits in the structured registration of the patients and the simplification of cross-institutional patient management, as patients can fulfil more tasks on their own and the health professionals can easily share data. The development of the Telematikinfrastructure of the Gematik offers opportunities to ease the digital connection between doctors' offices and the center for rare diseases. In particular, constant clarification and transparency are essential in order to provide information on data protection issues. Training and support should also be provided to promote patients' digital skills.