PAGOD syndrome is an extremely rare congenital malformation complex involving multiple organs. These include pulmonary artery and lung hypoplasia, diaphragm defects, omphalocele, sex reversal or ambiguous genitalia, and complex cardiac defects. Eight cases have been reported to date. We report a case of PAGOD syndrome that is manifested by right diaphragm eventration, horseshoe lung with right lung hypoplasia, hypoplastic left heart syndrome (mitral atresia, aortic atresia), scimitar syndrome, agonadism with ambiguous genitalia. A karyotype revealed normal 46-XY. This patient received a modified Norwood procedure for hypoplastic left heart syndrome as an initial palliation and bidirectional cavopulmonary anastomosis as a second stage of operation. The postoperative courses were uneventful. This patient is waiting for Fontan operation.