To investigate the association of rs72689236, a new functional single nucleotide polymorphism (SNP) of the gene encoding caspase-3 (CASP3), with the occurrence and development of Kawasaki disease by a meta analysis.A literature search was performed using databases at home and abroad according to inclusion and exclusion criteria, to acquire studies on the relationship between rs72689236 and Kawasaki disease published up to November 2012, including case-control studies and transmission disequilibrium tests. An integrated meta analysis was performed using RevMan 5.1 software after the studies were screened and evaluated.Six studies were extracted for systematic review of the association between rs72689236 and Kawasaki disease. The frequency of allele A of the SNP was significantly higher in patients with Kawasaki disease than in the controls (OR=1.34, 95%CI=1.24-1.46, P<0.001); the risk for Kawasaki disease in children with allele A (AA+AG) increased by approximately 44% compared with children with GG (OR=1.44, 95%CI=1.27-1.65, P<0.001). The frequency of allele A of the SNP was significantly higher in Kawasaki disease patients with coronary artery lesions than in those without coronary artery lesions (OR=1.51, 95%CI=1.10-2.07, P= 0.01); the risk for coronary artery lesions in Kawasaki disease patients with allele A (AA+AG) increased by approximately 59% compared with Kawasaki disease patients with GG (OR=1.59, 95%CI= 1.00-2.53, P=0.05]. No association between this SNP and the therapeutic effect of intravenous immunoglobulin (IVIG) was found in patients with Kawasaki disease.The allele A of functional SNP rs72689236 of CASP3 increases the risk for Kawasaki disease, and it may be used as the genetic marker for susceptibility to coronary artery lesions as a complication of Kawasaki disease. Currently, there is still no sufficient evidence that this SNP has an impact on the therapeutic effect of IVIG in patients with Kawasaki disease, and more studies are needed to investigate the feasibility of its application in individualized treatment.