Two patients with complex cyanotic congenital heart disease and without previous Glenn anastomosis underwent modified Fontan operations. Postoperatively, pulmonary arteriovenous malformations developed that resulted in cyanosis from significant intrapulmonary right-to-left shunting. These malformations were detected by pulmonary angiograms and contrast echocardiograms. Pulmonary arteriovenous malformations may be a major cause of late clinical deterioration in patients treated with modified Fontan operations.