Kawasaki disease (KD) is the major cause of acquired heart disease in children. KD is suspected of being an infectious disease, but the etiology has not yet been clarified. Immunologically, the disease is associated with the activation of T cells, monocytes, and macrophages resulting in highly elevated levels of several cytokines. Recently, expansions of T cells expressing TCRBV2 and TCRBV8 chains have been reported, and this suggests the involvement of a superantigen in the pathogenesis of KD. To address the role of a superantigen in KD, we investigated clonal expansion of T cells by estimating the complementarity-determining region 3 size profile among T cells expressing TCRBV1, TCRBV2, TCRBV4, TCRBV5, TCRBV8, TCRBV14, TCRBV16, TCRBV17, TCRBV18, and TCRBV20 chains during acute KD, during subacute KD, and during the long term follow-up period. During the acute phase of KD, several clonal expansions were found mainly in the CD8+ T cells that disappeared during the long term follow-up period. Our data suggest that the conventional Ags rather than a superantigen were involved in the pathogenesis of acute KD.