After surgery, the main concern for the partial AV septal patient is the degree of residual mitral valve insufficiency. The adult postoperative patient will generally have a mild heart murmur, indicating minor leakage (insufficiency) at the mitral valve. Angiography and/or echocardiography may be used to investigate the degree of insufficiency present. Sometimes (in 5-10% of cases), there will be the need for reoperation or valve replacement.

Occasionally (in less than 5% of cases), obstruction of the left ventricular outflow tract through subvalvar aortic stenosis (narrowing of the entrance into the aortic valve) will develop, requiring surgical intervention. In cases where this obstruction is suspected, echocardiography and/or cardiac catheterization procedures may be used to determine the severity of the problem. Sometimes, this obstruction may become recurrent and reconstructive surgery may become necessary. A modified Konno Procedure may be utilized, in which the aortic valve is replaced with a prosthesis or mechanical valve.

Conduction disturbances, such as complete heart block and atrial or ventricular arrhythmias, may occur. Therefore, patients should have periodic electrocardiograms (ECG).