A patient presenting with a history of transient ischemic attacks was initially diagnosed with a large secundum-type atrial septal defect by transesophageal echocardiography. Subsequent attempts to percutaneously repair the defect using an Amplatzer septal occlude device (AGA Medical, Plymouth, MN) failed to position correctly on multiple attempts. At the time of surgery, a largely deficient and highly fenestrated septum primum was found, which was likely the cause of the Amplatzer device (AGA Medical) failure. The defect was then definitively repaired using a bovine pericardial patch without incident.