Chromosome 22q11.2 deletion causes DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome with tetralogy of Fallot (TOF), and sporadic or familial TOF. To determine the prevalence and clinical importance of the 22q11.2 deletion in TOF, a series of 212 Japanese TOF patients was studied. The type of pulmonary blood supply, which may lead to various clinical outcomes, and other additional anomalies were evaluated clinically. The 22q11.2 deletion was diagnosed by fluorescence in situ hybridization with N25 and TUPLE1 probes. Of the 212 patients examined, 28 (13%) had a 22q11.2 deletion, the frequency being higher than that in TOF patients with trisomy 21. The prevalence of the deletion in TOF patients with pulmonary atresia (PA) plus major aortico-pulmonary collateral arteries (MAPCA) was significantly higher than the value in patients with PA plus patent ductus arteriosus (PDA) (P = 0.04) or with pulmonary stenosis (PS) (P < 0.0001). All 28 patients with 22q11.2 deletion had one or more extracardiac abnormalities. Four of 9 patients with the 22q11.2 deletion and TOF-PA-MAPCA suffered from bronchomalacia, while none of 19 patients with TOF-PA-PDA or TOF-PS manifested bronchomalacia (P = 0.006). These results indicate that 22q11.2 deletion is the most frequent cause of syndromic TOF, especially for TOF-PA-MAPCA, and bronchomalacia is the clinically most important associated anomaly in TOF-PA-MAPCA patients.