Objective　To investigate the association between nucleotide polymorphisms of GRIN3A gene and clinical characteristic of Kawasaki disease (KD) in children in Han population in central Chinese. Methods　A case-control study was performed. A total of 191 children with KD were recruited and 217 healthy children were served as controls. The distribution of SNP was determined by PCR-RFLP. Arterial lesions were detected by echocardiographic. Results　The distribution of three genotypes (CC, CG, GG) in SNP (rs7849782) was statistically difference between KD and control groups (P=0.034), and C allele was associated with KD susceptibility (OR=1.46, 95% CI: 1.10 - 1.92, P=0.007). In children with KD, the polymorphism of SNP loci was significantly associated with oral mucosa lesions and coronary artery lesion (P<0.05), but not associated with conjunctival hyperemia, hand-foot edema, rash, and lymphadenopathy (P>0.05). The polymorphism of SNP loci was also associated with the levels of erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) (P<0.05). Conclusion　The ploymorphism of SNP loci of GRIN3A gene (rs7849782) was associated with the susceptibility of KD. The C allele was the risk factors. The polymorphism of SNP was associated with oral mucosa lesions and coronary artery lesion, and may affect the levels of ESR and CRP.