Abstract: Rare diseases have a wide variety, complicated manifestations, and genetic and clinical heterogeneity, which make the diagnosis highly challenging.Moreover, many of the diseases lack effective therapies.The research in medical informatics technologies, such as clinical semantic system, genomic data analysis, imaging data analysis, and multi-omics data fusion analysis, has been greatly improved with the development of precision medical informatics, which is gradually breaking the restrictions of rare disease in data sharing and scientific research of rare diseases. Integrating and studying the shared data of rare diseases from different sources is conducive to the discovery of more pathogenic loci and the development of orphan drugs, which will promote the diagnosis and treatment of rare diseases. This review aims to introduce recent research progresses and applications of medical informatics technologies on rare diseases, in order to promote the development of medical informatics in the diagnosis and treatment of rare disease.