The Open Source Registry for Rare Diseases (OSSE) provides a concept and a software for the management of registries for patients with rare diseases. A disease is defined as rare if less than 5 out of 10,000 people are affected. Up to date, approximately 6,000 rare diseases are catalogued. Networking and data exchange for research purposes remains challenging due to the paucity of interoperability and due to the fact that small data stocks are stored locally. The so called “Findable, Accessible, Interoperable, Reusable” (FAIR) Data Principles have been developed to improve research in the field of rare diseases. Subsequently, the OSSE architecture was adapted to implement the FAIR Data Principles. Therefore, the so-called FAIR Data Point was integrated into OSSE to provide a description of metadata in a FAIR manner. OSSE relies on the existing metadata repository (MDR), which is used in to define data elements in the system. This is an important step towards unified documentation across multiple registries. The integration and use of new procedures to improve interoperability plays an important role in the context of registries for rare diseases.