There are more than 300 research groups for rare diseases in Japan. Although various clinical and genomic information of patients are being collected by the groups, the information is managed individually by each research group and the current practices for managing and sharing research data are not very efficient. Since “rare diseases” are literally rare, the understanding of the underlying disease mechanisms are incomplete and collecting a sufficient number of patients for clinical trials is difficult. Therefore, there is a need to collect and integrate the data and construct a data integration platform for rare disease research. Funded by the Japan Agency for Medical Research and Development, a national research and development project to establish a standard platform and supporting organization for rare disease registries in Japan is currently under way. In this article, we report the background, purpose, process, results, current status, and future plans of this project.