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Four patients with a thrombus in a coronary artery aneurysm due to Kawasaki disease (KD) were treated at our hospital between 1994 and 2009. All the cases were treated with intravenous coronary thrombolysis (IVCT) therapy and the cases with acute myocardial infarction were treated with additional intracoronary thrombolysis therapy. Although both thrombolytic therapies were effective, IVCT required more time than intracoronary thrombolysis to resolve the thrombus. We concluded that IVCT can be used as the first-line thrombolytic therapy for KD, except in cases with acute myocardial infarction.