Patients with major aortopulmonary collateral arteries (MAPCAs) often require additional surgical or catheter intervention after unifocalization (UF) due to stenosis and poor growth. We hypothesized that the UF design influences vascular growth; assessment was based on the passing route related to the bronchus. We enrolled 5 patients with pulmonary atresia (PA), ventricular septal defect and MAPCA who underwent UF and subsequent definitive repair at our institute from 2008 to 2020. Angiography and computed tomography scans were routinely performed before surgical intervention to clarify pulmonary circulation and the relationships between MAPCAs and the bronchus, which revealed peculiar MAPCAs directed to the pulmonary hilum passing behind the bronchus (defined as retro-bronchial MAPCAs; rbMAPCAs). Vascular growth of rbMAPCAs, non-rbMAPCAs and the native pulmonary artery were assessed using the angiograms before and after repair. The angiogram before UF [age 42 (24-76) days, body weight 3.2 (2.7-4.2) kg] showed that the diameter of the original unilateral PA, rbMAPCA and non-rbMAPCA was 19.95 ± 6.65, 20.72 ± 5.36 and 20.29 ± 7.42 mm/m2, respectively (P = 0.917). UF was completed in a single-stage with the placement of modified Blalock-Taussig shunt through median sternotomy at the age of 1.6 (1.0-2.5) months. Angiograms performed 3.0 (1.0-10.0) years after UF completion demonstrated a smaller rbMAPCA diameter at peri-bronchial region (3.84 ± 2.84 mm/m2) compared to the native unilateral PAs (16.11 ± 5.46 mm/m2, P < 0.0001) and non-rbMAPCA (10.13 ± 4.44 mm/m2, P = 0.0103). RbMAPCAs tend to be stenosed at the point where they cross the bronchus and emerge in the middle mediastinum after in situ UF.