Early challenges of atrial septal defect closure have decreased as repair techniques and modern era innovations developed, including the heart lung machine, myocardial protection techniques, and the intensive care unit. Today, complications are rarely encountered. However, occasionally, complications of embolism, stroke, and coronary insufficiency can occur if proper methods of deairing are not employed. Operative complications owing to unexpected anatomic variances can cause flow aberrations that can result in cyanosis, pathway obstruction, and arrythmias. A redundant Eustachian valve can complicate repair and cause inappropriate flow from the inferior caval vein to the left atrium, or in rare cases, occlusion of the inferior caval vein. Other documented complications involve superior caval vein syndrome caused by an expanding pericardial hematoma near the superior caval vein, impediments to flow owing to stenotic baffle construction, and overcoming the atrial anatomic characteristics that may require complex baffle preparation and implementation to avoid early and late atrial obstruction. This chapter reviews techniques to resolve possible complications experienced during repair.