Repair of truncus arteriosus often requires early right ventricular outflow tract (RVOT) reoperation. Using a modified repair, the branch pulmonary arteries are left in situ, which may avoid earlier RVOT reoperation. We hypothesized that our modified repair for type I and II truncus arteriosus would extend the time to RVOT reoperation. Infants with truncus arteriosus were divided into 2 groups: (1) traditional technique where the branch pulmonary arteries are excised from the truncal root, or (2) modified repair where the branch pulmonary arteries are left in situ and septated from the truncal root. Regardless of the approach, a bioprosthetic conduit or homograft was used to establish right ventricular to pulmonary artery continuity. Follow-up pulmonary artery angiograms were used to assess for branch pulmonary artery stenosis. From 54 infants (modified repair: 33, traditional technique: 21), there were no significant differences in age at repair, gender, or type of truncus arteriosus. With 100% follow-up, use of the modified repair resulted in a lower rate of branch pulmonary artery stenosis, and greater freedom from surgical branch pulmonary arterioplasty. Five- and 10-year freedom from RVOT reoperation (5 years: modified-81.5% vs traditional-30.5%, P = 0.004; 10 years: modified-53.3% vs traditional-30.5%, P = 0.01) favored the modified repair. Cox regression analysis demonstrated that the modified repair was associated with an independently lower risk for RVOT reoperation (hazard ratio: 0.08, confidence interval: 0.01, 0.75, P = 0.02). Thus, maintaining the branch pulmonary artery architecture resulted in greater freedom from RVOT reoperation.