A normal lung is supplied by a pulmonary artery branching from the pulmonary trunk. Major aorto-pulmonary collateral arteries (MAPCAs) are found in combination with various congenital heart malformations such as pulmonary atresia with ventricular septal defect (PA-VSD). Now that MAPCAs are used for unifocalization in patients with PA-VSD, the question arises as to whether the morphologic criteria of these collateral arteries could help to provide better results. We compared the morphology of the pulmonary vascular bed, the origin, course and connections of the MAPCAs in 40 consecutive infants with PA-VSD with or without 22q deletion (del22q11.2.). All underwent echocardiographic evaluation and catheterization. Identification of del22q11.2. was performed by FISH study. Del22q11.2. was identified in 16 pts (40%); the presence of MAPCAs was significantly higher in patients with del22q11.2. (9/16 vs 3/24, p = 0.01). While complex morphology of MAPCAs, anastomoses with the central pulmonary artery outside the lung and absent ductus arteriosus were associated with del22q11.2, confluence of the pulmonary arteries was not a relevant phenotypic difference. The size of the right and left pulmonary arteries expressed as a standard deviation difference of the normal range for body surface area was -4.2 (quartiles -3.1/-1.8) for PA-VSD with del22q11.2. and -2.6 (quartiles -5.3/-2.9) for PA-VSD without del22q11.2. (p = 0.02). The difference between measured and theoretical Nakata index was -373 +/- 94 for PA-VSD with del22q11.2. vs. -245 +/- 93 for PA-VSD without del22q11.2. (p = 0.0002). A specific pulmonary vascular bed phenotype could be defined in patients with PA-VSD with del22q11.2. deletion: MAPCAs with complex loop morphology and small but confluent central pulmonary arteries. These findings indicate a different timing of the faulty development pathway of the pulmonary vascular bed in patients with and without del22q11.2. This phenotype difference may help our understanding of maldevelopment and facilitate decisions concerning the suitability of these arteries for unifocalization procedures.