Kawasaki disease (KD) is a leading cause of acquired cardiac disease of children in the developed countries. The pathogen that triggers this perplexing disease is still unknown after 40 y from the first description. Epidemiologic findings have made us believe that there are considerable genetic components in the etiology and some candidate genetic variations, which confer susceptibility to KD or risk for coronary artery lesions have been identified. However, most of them remain to be definitively confirmed by replication studies with large cohorts. In this article, I review the candidate gene association studies to date. I also introduce our recent findings in genome-wide approach, which revealed the importance of Ca2+/nuclear factor of activated T-cells pathway in the pathogenesis of KD.