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The association of conotruncal heart defects with 22q11.2 chromosomal microdeletions is well established. However, it is not clear whether particular types of conotruncal malformations or additional cardiovascular anomalies are associated with microdeletions. In addition, cardiac surgery outcome in children with conotruncal defects and del22q11.2 is not well described. We prospectively enrolled 214 children with conotruncal defects: 126 with tetralogy of Fallot (TOF), 18 with pulmonary atresia-ventricular septal defect (PA-VSD), 15 with truncus arteriosus communis (TAC) type I, one with interrupted aortic arch (IAA) type B, and 54 with the transposition of great arteries, who were consecutively hospitalized at the Pediatric Cardiology Department between 2003 and 2005. 22q11.2 microdeletion was identified by fluorescence in situ hybridization. The postoperative course following cardiac surgery was compared in patients with TOF and its more severe form, PA-VSD, with/without del22q11.2 (groups A and B) and TAC with/without del22q11.2 (groups C and D). In 15 of 214 patients, 22q11.2 microdeletion was diagnosed (in 11 with TOF/PA-VSD, in three with TAC, in one with IAA type B). In patients with TOF/PA-VSD and microdeletion anatomic features that were significantly associated with 22q11.2, deletion included right aortic arch (p = 0.018), aberrant right subclavian artery (p < 0.001), and major aortopulmonary collateral arteries (p = 0.016). A complicated postoperative course was more frequent and mortality was higher in patients with conotruncal defects and with/without microdeletion. We conclude that additional cardiovascular anomalies are significantly more frequent in children with 22q11.2 microdeletion and TOF/PA-VSD. Children with conotruncal heart defects and 22q11.2 microdeletion more frequently experienced complicated postoperative course after cardiac surgery.