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Specific types and subtypes of cardiac defects have been described in children with 22q11.2 deletion syndrome as well as in other genetic syndromes. The conotruncal heart defects occurring in patients with 22q11.2 deletion syndrome include tetralogy of Fallot, pulmonary atresia with ventricular septal defect, truncus arteriosus, interrupted aortic arch, isolated anomalies of the aortic arch, and ventricular septal defect. These conotruncal heart defects are frequently associated in this syndrome with additional cardiovascular anomalies of the aortic arch, pulmonary arteries, infundibular septum, and semilunar valves complicating cardiac anatomy and surgical treatment. In this review we describe the surgical anatomy, the operative treatment, and the prognostic results of the cardiac defects associated with 22q11.2 deletion syndrome. According to the current literature, in patients with tetralogy of Fallot with/without pulmonary atresia and truncus arteriosus, in spite of the complex cardiac anatomy, the presence of 22q11.2 deletion syndrome does not worsen the surgical prognosis. On the contrary in children with pulmonary atresia with ventricular septal defect and probably in those with interrupted aortic arch the association with 22q11.2 deletion syndrome is probably a risk factor for the operative treatment. The complex cardiovascular anatomy in association with depressed immunological status, pulmonary vascular reactivity, neonatal hypocalcemia, bronchomalacia and broncospasm, laryngeal web, and tendency to airway bleeding must be considered at the time of diagnosis and surgical procedure. Specific diagnostic, surgical, and perioperative protocols should be applied in order to provide appropriate treatment and to reduce surgical mortality and morbidity.