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Kawasaki disease (KD) is an acute febrile illness of early childhood caused by vasculitis. Whether or not peripheral blood T cells are activated in acute KD remains uncertain, as some reports have presented evidence of peripheral blood T cell activation, whereas others suggest that the level of peripheral blood T cell activation is low during acute KD. Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4, CD152) is a surface molecule of activated T cells. We therefore investigated intracellular CTLA-4 expression in the peripheral blood T cells of patients with acute KD as a marker of T cell activation. We collected blood samples from 20 patients with KD and six with Epstein–Barr virus infectious mononucleosis (EBV-IM) who were admitted to our hospital, as well as 13 healthy children. We determined the intracellular expression of CTLA-4 in T cells by flow cytometry. We demonstrated that the intracellular expression of CTLA-4 is up-regulated in peripheral blood CD3+ T cells, CD4+ T cells and CD8+ T cells at the early part of the acute stage in KD. However, the mean percentages of intracellular T cells expressing CTLA-4 in EBV-IM patients were about fourfold higher than those in T cells from patients with acute KD. Our results suggested that the level of activation of peripheral blood T cells is very low during acute KD.