Kawasaki disease (KD) is a multisystemic vasculitis that often includes coronary artery involvement. The serum levels of matrix metalloproteinase (MMP)-3 and -9 are significantly elevated in KD patients, and polymorphisms in the genes encoding MMP-3 and MMP-9 have been associated with the susceptibility, severity, and progression of atherosclerosis and aneurysm. However, the association between MMP-3 gene polymorphisms and development of aneurysm is somewhat controversial in a number of diseases. Ninety-seven children with KD and 194 children with congenital heart disease (CHD) were included in this study. Echocardiography was used to examine all children in the KD group for coronary artery aneurysm. Genotyping of the MMP-3 (-439C/G) promoter polymorphism was performed using the single-base extension method, and serum MMP-3 levels were estimated using the sandwich enzyme immunoassay method. There was no significant difference in MMP-3 (-439C/G) genotypes between KD and control groups. There was no association between this MMP-3 polymorphism and development of coronary aneurysm in KD. Serum MMP-3 levels were significantly higher in KD patients compared to control subjects. Among the KD patients, serum MMP-3 levels were higher in children with genotypes CG+GG compared to the CC group, but this difference was not significant. Although further large-scale studies will be required to fully examine the relationship between MMP-3 gene polymorphisms and coronary artery lesions (CAL) in KD, the present findings suggest that while MMP-3 may play a role in the pathogenesis of KD, there is no apparent association between CAL and the MMP-3 (-439C/G) gene polymorphism in Korean children with KD.