Kabuki syndrome (KS), a rare congenital disorder occurring in approximately one in 32 000 births, is primarily associated with mutations in the KMT2D or KDM6A genes. [1][2][3][4] The presence of autoimmune disorders, such as immune thrombocytopenia (ITP), which occurs in 7.3% of cases, 5,6 seriously complicates the clinical management and understanding of KS. Reports of KS co-occurring with ITP and autoimmune thyroiditis (AIT) are rare. KMT2D mutation type significantly influences disease phenotype and severity, 2 highlighting the importance of mutation identification for predicting disease phenotypes and autoimmune complications, especially in prenatal diagnosis. Here, we present a rare case of KS with a novel pathogenic KMT2D mutation, featuring delayed linguistic, cognitive and physical development, extensive somatic and organ malformations and severe ITP and AIT. This study improves our understanding of KS genetics and the development of treatments tailored to diverse comorbidities.Whole-exome sequencing (WES) was conducted on peripheral blood mononuclear cells. The three-dimensional structure of mutant KMT2D protein, predicted using SWISS-MODEL, 7 was compared with the wild-type protein in Protein Data Bank. Sanger sequencing was performed to confirm the mutation and familial pedigree. The clinical and molecular characteristics of KS accompanied by ITP were summarized based on previous reports (Supplementary Methods).A 9-year-old boy presented with persistent unexplained oral bleeding and cutaneous purpura for 4 days in May 2022. Despite initial treatment with intravenous immunoglobulin (IVIG, 15 g/day for 2 days) and platelet infusion at a local hospital, his platelet count declined from 16 × 10 9 /L to 1 × 10 9 /L with haematuria. His history included post-birth cleft palate repair and no known familial haematological or developmental disorders. Prior to conception, his father received treatment for post-traumatic epilepsy with antiepileptics. And his mother was diagnosed with lung cancer. Physical examination revealed language and cognitive delays, short stature (weight: 28.3 kg, height: 117.0 cm) and abnormal facial features (e.g. elongated palpebral fissures, lower eyelid ectropion, hypertelorism, prominent auricles, Figure 1A,B), craniofacial development (cleft palate, diastema, Figure 1C), musculoskeletal system (brachydactyly, camptodactyly,