The purpose of this study is to investigate the association of programmed death-1 gene (PD-1) polymorphisms with genetic predispositions to Kawasaki disease (KD). A total of 73 patients with KD and 100 healthy controls were enrolled from 2007 to 2008. Two single nucleotide polymorphisms of the PD-1 gene, rs41386349 and rs2227981, were analyzed. Higher T allele frequency of rs41386349 was found in the patient group than the control group (p = 0.007, odds ratio (OR) = 1.9, 95% CI = 1.2-2.9). PD-1 rs2227981 polymorphism was not significant in patients with KD comparing with the control group (p = 0.4, OR = 1.2 (0.8-1.9)). Furthermore, no difference of PD-1 polymorphisms between patients with coronary artery dilatation (CAD) and those without CAD was found. Our data support the possibility that PD-1 gene polymorphism may be related with the genetic susceptibility of KD in Korean population.