Objective To investigate the association between nucleotide polymorphisms (rs1569723 in CD40 gene) and clinical characteristics in Kawasaki disease (KD) in Han Chinese children. Methods A case-control study was performed,and 179 children with KD and other 197 normal children served as controls were included. The SNP genotypes were detected using PCR-RFLP, and all data were analyzed by SPSS 19.0. Results It was found that the SNP (rs1569723) was associated with KD (P=0.048), and the frequency of A allele in KD group was higher than that in control group (OR=1.505, 95%CI:1.095-2.070, P=0.012). SNP genotypes were associated with rash and lymphadenopathy (P=0.041, 0.047), but not associated with conjunctival hyperemia, hand-foot edema, oral mucosa lesions, and coronary artery lesion (P=0.688,0.758, 0.557, 0.552). Conclusions Genotypes of SNP (rs1569723) were associated with KD susceptibility, and A-allele is a risk allele. The SNP loci might be associated with rash and lymphadenopathy in KD in Han Chinese.