Pulmonary thrombus formation in the region of atrial anastomosis following lung transplantation has been reported by several authors. Such patients typically present immediately after surgery with significant hemodynamic compromise causing pulmonary edema and hypoxemia. We describe a patient who presented with bilateral neurologic deficits 4 and 6 weeks after lung transplantation. Despite a normal transthoracic echocardiogram, transesophageal echocardiography (TEE) detected a large left atrial thrombus adherent to the atrial anastomosis. This thrombus was treated with intravenous heparin and subsequently warfarin. After 3 weeks, a repeat TEE demonstrated complete resolution of the lesion. This case demonstrates that postoperative left atrial and pulmonary venous thrombi may provide the basis for serious patient morbidity without hemodynamic or radiographic clues to their presence, that TEE is superior to transthoracic echocardiography for detecting left atrial thrombi, and that such lesions can respond to medical management alone.