The diagnosis and treatment of rare diseases is one of the important challenges in the global medical field. In the recent years,with the rapid development of science and technology and the promulgation of relevant policies,great progress has been made in the field of diagnosis and treatment of rare diseases. This review focuses on the application of molecular diagnostic technology and the interpretation of genetic variation in the process of accurate diagnosis of rare diseases. It is carried out in combination with several reports in this special issue. It is hoped that this issue can provide a reference for the diagnosis and treatment of rare diseases.