This report concerns a 10-month-old infant with subtotal cor triatrium associated with left sided partial anomalous pulmonary venous connection to the innominate vein. In the operation, we found that the fossa ovalis existed between the right atrium and the accessory atrial chamber. We performed a radical operation which consisted of a resection of the intra-left-atrial diaphragma and a anastomosis of the vertical vein to the left atrium. His postoperative course was uneventful, and the result was satisfactory. We have presented and reviewed our case, and then discussed the embryogenesis and the hemodynamics. To our knowledge, our case represents the first successful surgical repair of this combination of defects in Japan.