The objectives of this study were to evaluate changes in dimension of the neo-aortic annulus, aortic root, and aortic anastomosis following arterial switch operation (ASO) and to identify risk factors for developing abnormal neo-aortic root enlargement and aortic regurgitation (AR). Prior studies report development of neo-aortic root dilatation and AR in a small subset of patients after ASO. Predisposing factors for neo-aortic root dilatation and development of moderate/severe AR are poorly understood. We performed a retrospective review of all patients with d-transposition of the great arteries (d-TGA) or double-outlet right ventricle with subpulmonary ventricular septal defect (VSD) who underwent ASO from May 1986 to January 2001. Serial echocardiograms were reviewed to measure neo-aortic annulus, root, and anastomosis diameter (z scores) and to determine progression of AR. Potential risk factors were assessed for developing neo-aortic root enlargement and AR. There were 119 patients (44 female and 75 male): 73 patients had simple d-TGA, 36 had d-TGA with ventricular septal defect, and 10 had a Taussig–Bing heart. The median duration of follow-up was 65 months (range, 12–180). The median neo-aortic root (z = 0.55 ± 2.2; p < 0.01) and aortic annulus dimensions (z = 1.57 ± 1.75; p < 0.01) were significantly increased over the study period. Aortic anastomosis diameter correlated with growth of the ascending aorta (z = 0.55 ± 1.24). Development of severe neo-aortic root enlargement was associated with prior pulmonary artery (PA) banding (p < 0.01), the presence of a VSD (p = 0.03), and Taussig–Bing anatomy (p < 0.01) but was independent of coronary arterial anatomy, coronary arterial transfer technique, or associated lesions (p > 0.05). At latest follow-up, there was no or trivial AR in 88 patients, mild AR in 29 patients, and moderate to severe AR in 3 patients. Risk factors for developing mild or worse AR included severe or rapid neo-aortic root dilatation (p < 0.01). Only 3 patients required surgical intervention for AR. Despite the significant prevalence of neo-aortic root enlargement at intermediate follow-up after ASO, there is a low incidence of significant AR. Prior PA banding, the presence of VSD, and Taussig–Bing anatomy are risk factors for severe root enlargement. Surgical intervention for AR was rare (2%), however, serial surveillance of such patients is vital to monitor for neo-aortic root enlargement and potential aortic valve dysfunction.