Cor triatriatum is a rare congenital anomaly which has wide-ranging severity depending on the structure of the additional intra-atrial septum. We report the case of a boy who was incidentally diagnosed with cor triatriatum by echocardiography during diagnosis and treatment of Kawasaki disease. He has had no definite life-threatening symptoms except recurring respiratory infections. Serial follow-up of such patients is mandatory to check for the potential risks related to the anomalous inter-atrial structure.