A 32-year-old woman underwent transcatheter closure of a secundum type atrial septal defect with the Amplatzer device. The procedure was started under premedication with aspirin, clopidogrel, and heparin. During the procedure, a highly mobile thrombus attached to the left atrial disc of the device was detected by transesophageal echocardiography (TEE). The device and the associated thrombus were successfully withdrawn and the patient was started on a combination of heparin and tirofiban infusion. The procedure was successfully completed without any recurrent thrombus formation or residual shunt. Further investigation for thrombophilia revealed homozygous factor V Leiden mutation and the patient was started on a life-long warfarin therapy. Follow-up TEE showed proper device position with no recurrent thrombus and the follow-up was uneventful.