Coronary artery anatomy represents a challenging and, often, determining predictor of outcome in an arterial switch operation (ASO). Impact of specific coronary artery variants, such as single, intramural and inverted, on time-related events following ASO, is, yet, to be determined. We sought to compare early and late outcomes within the group of nonstandard coronary artery variants. Patients who underwent ASO from January 1995 to October 2010 were reviewed. Patients with coronary artery variants other than L1Cx1R2 (“standard” by Leiden classification) were included. Patients with single, intramural and inverted coronary artery variants incorporated in group A. All other nonstandard coronary variants incorporated in group B. Demographics, perioperative variables, early and late outcomes were assessed. Of the 123 ASO, 24 patients (19.5%) with nonstandard coronary variant were studied. Thirteen were in group A and 11 in group B. There were two early deaths (1 in group A and 1 in group B) (p > 0.05). There is one death early after hospital discharge (group A). Mean follow-up was 59.4 ± 55.1 months. There was no structural coronary artery failure after hospital discharge following ASO. Freedom from any reintervention at 8 years was (78.3 ± 9.6%) (p 0.55) with no late neo-aortic or mitral valve intervention. ASO with single, intramural or inverted coronary artery course carries no added longitudinal risk for structural or flow impairment within the group of nonstandard coronary artery variants. There is an early hazard period with no late survival attrition. Aortic arch repair as part of staged strategy prior to ASO might influence early and late outcome.