Objective: Congenital heart defects with major aortopulmonary collateral arteries show marked variability in the size and distribution of native pulmonary arteries. We sought to classify the size and distribution of native pulmonary arteries and to determine their influence on surgical outcome. Methods: Between 1989 and 2002, 164 patients underwent surgical intervention for congenital heart defects with major aortopulmonary collateral arteries (median age, 10 months). Three patterns of native pulmonary arteries were identified: intrapericardial native pulmonary arteries present (group I); confluent intrapulmonary native pulmonary arteries without intrapericardial native pulmonary arteries (group II); and nonconfluent intrapulmonary native pulmonary arteries (group III). Thirty-seven (23%) patients had single-stage and 76 (47%) patients had multistage complete repair. Thirty (18%) patients await septation, and 8 (5.0%) patients are not septatable. Follow-up is 98% complete (median follow-up, 5.8 years). Results: In the 164 patients there were 15 (9.1%) early and 12 (7.3%) late deaths. Early mortality after complete repair was 4.4% (n = 5). Actuarial survival was 90% ± 3% and 85% ± 4% at 1 and 10 years, respectively. Actuarial freedom from surgical or catheter reintervention in septated patients was 77% ± 4% and 45% ± 8% at 1 and 10 years, respectively. On multivariate analysis, the morphology of the native pulmonary arteries was the only factor that influenced actuarial survival after complete repair (P = .04). Group III had the highest risk of death after septation (P = .008). Group II fared better than group III after the initial operation (P < .05). Conclusions: Current classifications of congenital heart defects with major aortopulmonary collateral arteries are based on the presence or absence of intrapericardial pulmonary arteries. We have identified a subgroup without intrapericardial native pulmonary arteries but with confluent intrapulmonary native pulmonary arteries. This group has a better outcome than those with nonconfluent intrapulmonary native pulmonary arteries.