Juxtaposition of atrial appendages is a rare cardiac congenital anomaly, usually associated with other cardiac malformations. Until now, it has not been linked to any significant clinical implications. We report cardiovascular magnetic resonance (CMR) findings of two adult patients who underwent atriopulmonary Fontan operation in the setting of left juxtaposition of the atrial appendages. The patients were in sinus rhythm at the time of the CMR study. Both patients had episodes of sustained atrial tachyarrhythmia requiring electrical cardioversion and were anticoagulated with warfarin with target INR 2-3. CMR images showed a thrombus located in the enlarged and juxtaposed right appendage in both patients. Blood flow frequently appears slow or sluggish in the dilated right atrium following atriopulmonary Fontan surgery. In addition, cine CMR suggested that blood flow reaches very low velocities in the massively dilated juxtaposed right atrial appendage cul-de-sac, thus potentially creating a substrate for clot formation. These findings propose that juxtaposed atrial appendages in atriopulmonary Fontan is an additional risk factor for clot formation, specifically in the dilated right atrial appendage on the left side juxtaposed with the left atrial appendage and that prophylactic anticoagulation is highly justified in these patients.