We describe a rare type of atrioventricular septal defect with common atrioventricular orifice and malaligned atrial septum, the latter feature resulting in severe obstruction of the left atrial egress. Excision of the atrial septum and banding of the pulmonary trunk was performed at the age of thirteen months. Lung biopsy demonstrated marked medial hypertrophy with severe intimal fibrosis in the small pulmonary arteries and mild thickening of the pulmonary veins, considered contraindications for corrective surgery.