The population of neonates and children with congenital heart defects presents about a 30% prevalence of associated genetic syndrome or additional extracardiac anomalies and may show an increased risk of death or major complication at cardiac surgery. Since a well-defined pattern of combined cardiac and extracardiac anomalies may be found in relation to specific genetic defects, correct understanding of the genetic issues may help improving diagnosis, surgical approach and final outcome of these patients. Hereby we review the medical and surgical issues correlated to the genetic asset in patients with congenital heart defects and genetic syndromes, including trisomy 21, deletion 22q11, Noonan/LEOPARD, Turner, Marfan and Williams syndromes. Recognition of specific surgical risk factors can lead to the preparation of specific diagnostic and perioperative protocols in order to reduce operative mortality and morbidity.