Kawasaki disease (KD) is an acute systemic vasculitis syndrome that predominantly affects children younger than 5 years of age, and may causes serious, sometimes life-threatening, cardiac sequela associated with coronary artery aneurysm (CAA). To identify genetic variants that confers a highly increased risk of coronary artery aneurysm-related in Kawasaki disease. In this study, we carried out genome-wide association study (GWAS) in a Korean children population including 102 CAA-related KD cases and 126 controls. Fifteen genetic loci were found to be significantly correlated with KD risk (P<1.0X10(-7)). Our case-control study revealed that rs4236089 C allele in chloride intracellular channel 5 (CLIC5) gene at 6p21.1 was significantly associated with KD patients with CAA (odds ratio (OR)=4.6, P=7.53X10(-7)). These findings suggest that the CLIC5 gene may play a crucial role in CAA development pathway of KD.