BACKGROUND: Kawasaki disease (KD), an acute vasculitis syndrome affecting children under 5 years, lacks specific biological markers for diagnosis. This study explores immune cell activation in KD patients during early vasculitis symptoms to identify potential diagnostic markers and guide intravenous immunoglobulin (IVIG) therapy timing. METHODS: The study included single-cell sequencing (SCS) from 10 patients, comprising seven with KD and three controls, as well as flow cytometry and polymerase chain reaction (PCR) validation from 277 patients. This included 95 children with KD and controls consisting of 12 healthy children and 170 children with febrile illnesses. Children with KD were divided into early vasculitis group and late vasculitis group based on whether the symptoms of vasculitis were less than or more than three days. peripheral blood mononuclear cells (PBMCs) were sequenced using the 10× Genomics platform, and flow cytometry and quantitative PCR (qPCR) verified changes in gene expression and cell proportions. RESULTS: KD patients showed higher CD19 CONCLUSIONS: This study highlights the close relationship between the number of immune cells and gene expression changes with the duration of vasculitis in KD, providing new insights into the pathophysiological mechanisms of the disease and potential prognostic indicators for clinical treatment.