Abstract Background BaMaRa allows the secure collection and deidentified centralization of medical data from all patients followed-up in a rare disease expert network in France, based on a minimum data set (SDM-MR). The present article describes BaMaRa information system implementation and development across the whole national territory as well as data access requests through BNDMR, the data warehouse which centralizes all BaMaRa data, during the 2015–2020 period. Materials and Methods SDM-MR is made up of 60 interoperable items and is routinely collected through BaMaRa in rare disease centers as part of care and discharged into BNDMR after deidentification and data reconciliation. Data access is regulated by a scientific committee. Results In total, 668 002 affected patients had an SDM-MR recorded in BNDMR by the end of 2020 with a mean value of 3.4 activities per patients. Data access was provided for 66 projects. Conclusion The BaMaRa-BNDMR infrastructure provides an administrative and epidemiological resources for rare diseases in France.