AbstractCapsule: HLA‐B associated transcript (BAT) 2, 3, and 5 polymorphisms and haplotypes are associated with Kawasaki disease (KD) and coronary artery aneurysm (CAA) formations. Objective: KD, an acute vasculitis with unknown etiology, involves a complex interaction of immuno‐inflammatory process, cytokines activation, and genetic factors. We aimed to investigate if genetic variants of human lymphocyte antigen (HLA)‐BAT2, 3, and 5 (BAT2, 3, and 5) could be used as markers of susceptibility in KD and CAA. Methods: Individuals were divided into three groups: (1) normal controls; (2) KD with CAA; and (3) KD without CAA. Polymorphisms for BAT2 (−8671, 16483), BAT3 (8854, 2–24), and BAT5 (22655, 9569) were genotyped by PCR system with TaqMan allelic discrimination assay. Genotype/allelic frequencies and haplotypes (BAT2−8671‐BAT216483‐BAT38854‐BAT32–24‐BAT522655‐BAT59569) in each group were compared. Results: Genotype distribution and allele frequency of BAT2 −8671, BAT3 8854, and BAT5 22655, 9569 polymorphisms in each group were significantly different. BAT2 −8671*G, BAT3 8854*C, BAT5 22655*C, and 9569*A‐related genotypes and alleles are correlated with the developments of KD and CAA. BAT haplotypes of ATTGTG and ATCATG are associated with higher susceptibilities of KD with CAA susceptibility. Conclusion: BAT2 −8671, BAT3 8854, and BAT5 22655, 9569 polymorphisms as well as BAT haplotypes (ATTGTG and ATCATG) might be associated with higher KD susceptibility and CAA formation. HLA‐B region polymorphisms might contribute to the pathogenesis of KD and CAA. J. Clin. Lab. Anal. 24:262–268, 2010. © 2010 Wiley‐Liss, Inc.