Although the etiology of Kawasaki disease (KD) still remains unknown, the epidemiologic findings have suggested the existence of genetic factors of KD. To identify susceptibility genes for KD, we conducted affected sibpair analysis using 78 Japanese KD families and found positive linkage signal in 10 chromosomal loci. We are now performing linkage disequilibrium mapping using single nucleotide polymorphisms (SNPs). In one locus we identified SNPs significantly associated with KD in the Japanese and also in the U.S. population. We hope that our ongoing investigation of the function of the SNP (s) and the gene in which these SNPs locate will lead further understanding of the disease and pave the way to a new therapeutic strategy.