We report the unexpected transesophageal echocardiography (TEE) finding of a left atrial (LA) thrombus near the end of cardiopulmonary bypass and after deployment of an AtriClip (Atricure, Inc, Westchester, OH) in an 84-year-old man with atrial fibrillation and aortic stenosis undergoing aortic valve replacement and LA appendage ligation. TEE examination before cardiopulmonary bypass and deployment of the AtriClip had not shown a thrombus in the LA appendage. The heart was rearrested and thrombus was successfully removed through a left atriotomy. This case emphasizes the importance of careful TEE examination for dislodged thrombi after surgical manipulation of the LA appendage.