We used a selective DNA amplification technique to detect Epstein-Barr virus (EBV) DNA in peripheral blood mononuclear cells from patients with Kawasaki disease (KD). By means of the polymerase chain reaction EBV sequences were indentified directly in 21 (60%) of 35 KD patients within 2 weeks after the onset of KD. Furthermore, EBV sequences were detected in all of 6 repeatedly tested patients with KD within 3 months after disease onset. In contrast, only 2 (12%) of 17 control DNA samples were polymerase chain reaction positive. These results indicate that an unusual EBV-cell interaction may exist in KD.