Abstract: 　Objective　To explore the mechanism of intravenous immunoglobulin (IVIG) treatment on Kawasaki disease (KD). Methods Thirty-six KD patients and 13 patients with pneumonia or upper respiratory infection (control group) were selected. The gene expression profiles of peripheral white blood cells from 4 KD patients (three male, one female) pre-and post- IVIG therapy and one pneumonia patient (male) were analyzed by Agilent gene chip. The gene expression was detected in 32 KD patients and 12 control patients by real-time PCR. Results The expressions of IL-1β, S100A9, S100A12 and MMP9 were significantly down-regulated in response to IVIG. The expressions of IL-1β, S100A9, S100A12 and MMP9 mRNA were significantly different among pre-treatment, post-treatment and control groups (P<0.01). The expressions of IL-1β and MMP9 mRNA were significantly down-regulated in response to IVIG (P<0.01). The expression of IL-1β mRNA was significantly higher in KD patients than that in control group. The expression of MMP9 mRNA was significantly higher in KD patients pre and post treatment than that in control group (P<0.01). The expression of MMP9 mRNA was significantly higher in KD patients complicated with coronary artery lesion (CAL) than that in KD patients without CAL complication (P=0.001). Conclusions The effects of IVIG on KD may be mediated by IL1B, S100A9, S100A12 and MMP9. MMP9 gene expression may be related to complication of CAL in KD.