PURPOSE: Kawasaki disease is an acute systemic vasculitis syndrome of children. Although its etiology is largely unknown, epidemiological findings suggest that genetic factors play a role in the pathogenesis of Kawasaki disease. We investigated differentially expressed genes in Kawasaki patients. METHODS: we extracted bloods of Kawasaki patients in acute, subacute, convalescent phase and normal control group. Gene expressions were investigated by annealing control primer (ACP)-based GeneFishing PCR. Products were visualized after electrophoresis in 2% agarose gel and automatically sequenced. RESULTS: 165 differentially expressed genes were identified by using 120 ACPs. Expression of immunoglobulin kappa and lambda (DEG 20,45,54) significantly was down-regulated in acute and subacute phase of Kawasaki disease but up-regulated in convalescent phase. Apollon gene (DEG 64) was down-regulated in kawasaki patients. TNIK and other DEGs were also found. CONCLUSION: This findings suggest that different genetic change occur in the coarse of Kawasaki disease. Further study of differentially expressed gene using annealing control primer system may provide etiology and pathogenesis of Kawasaki disease.