A 6-day-old male with interruption of the aortic arch at the isthmus (type A) had the typical phenotype of DiGeorge syndrome. There was also a doubly committed juxta-arterial ventricular septal defect and an unobstructed left ventricular outflow tract. Hypoplasia of the thymus was confirmed during a modified Blalock-Park operation. He had persistent hypocalcemia, and was susceptible to infection. He was subsequently revealed by the use of fluorescence in situ hybridization analysis to have 22q11.2 deletion. Interruption of the aortic arch at the isthmus is presumed to reflect abnormal fetal hemodynamics, and is considered a distinct pathogenetic entity from interruption between the left common carotid and subclavian arteries, the latter being the variant more frequently associated with DiGeorge syndrome. In our case, the 22q11.2 deletion likely played a major role in the etiology of the interrupted aortic arch.