Abstract: Rare kidney diseases are important causes of chronic kidney disease (CKD) in children. The majority of rare kidney diseases in children are hereditary kidney diseases, accounting for about 29.7% to 52.1% of children with CKD. Next-generation sequencing has been widely used in clinical diagnosis in the past decade, leading to the improvement of the diagnosis of hereditary kidney diseases. In 2018, China announced the first list of rare diseases and greatly enhanced the diagnosis, treatment and research of rare diseases in China, including rare kidney disease. Meanwhile, China faces great challenges in the diagnosis and treatment of hereditary kidney diseases in Children, including the assessment of pathogenicity of gene variants, the lack of biomarkers for disease progression and therapy efficacy, lack of drugs, and others. The future lies in the cooperation between patients, physicians, researchers, and health policy markers, and the fast translation from research finding to clinical application, so as to meet the demand from the children with rare kidney diseases in China.