Abstract Transesophageal echocardiography demonstrated six instances of venous thrombus formation in the inferior vena cava, right atrium and caval-pulmonary anastomosis region in four children after a modified Fontan operation. Transthoracic surface echocardiography failed to identify these thrombi in five of the six cases because of the posterior location of the thrombus or imaging interference from surgical hardware. These thrombotic episodes occurred 2 days to 5 years after the Fontan operation in children 25 to 168 months of age. Clinical features of compromised cardiac performance with cyanosis or inadequate perfusion were present during four of the six episodes. In two patients, thrombi occurred around transvenous permanent atrial pacing leads. Therapy to eliminate thrombus included surgery (two cases), anticoagulation with warfarin (three cases) and streptokinase thrombolysis (one case). Disappearance of the thrombus was confirmed by transesophageal study in three of the four cases with follow-up echocardiography. Transesophageal echocardiographic demonstration of atrial and pulmonary thrombi that could not be seen by transthoracic imaging suggests that these thrombi occur with greater frequency in patients who have undergone the Fontan operation than was previously suspected.