Objective The purpose of this study is to explore and evaluate the clinical characteristics of children with different rare diseases by using the database of children's rare diseases in our hospital, so as to provide a basis for promoting the prevention, diagnosis and treatment of children with rare diseases. Methods The data of children in our rare disease database (Phase I) were analysed from 16th May 2011 to 29th January 2023 by child admission. The International Classification of Diseases (ICD-10) was used to classify and count the number of cases mined, gender, geography, age, genetic tests, repeat visits and hospitalisations. Results A total of 3491 children were included in the database, covering 20 rare diseases, representing 9.7% (20/207) of the rare disease catalogue. The ratio of male to female patients was 1.30:1 (1975 males/1516 females). Methylmalonic acidemia (1024 cases, 29.33%), congenital adrenocortical hyperplasia (944 cases, 27.04%) and phenylketonuria (191 cases, 5.47%) were the top three rare diseases. Genetic testing data were included in 220 cases, accounting for 6.30% of the total number of diseases. Hospitalised cases covered 16 provinces, with Henan province accounting for 96.60% of cases (1988/2058). Rare diseases in infancy accounted for 42.36% (1479/3491) of the total number of cases. Multiple osteofibrous dysplasia with precocious puberty syndrome was the highest percentage of repeat hospitalisation for rare diseases at 24.24% (8/33), while children with Kalman syndrome had the highest rate of repeat outpatient visits at 51.85% (14/27). Conclusion Based on the database of special diseases, we analyzed the clinical characteristics of 20 rare diseases in children, which provided a reference for promoting the prevention, control, detection and research of rare diseases in children in our province.