Aortic arch abnormalities are uncommon in patients with congenitally corrected transposition of the great arteries. Over a 20-year period, 10 patients with congenitally corrected transposition and Ebstein's anomaly of the systemic atrioventricular (AV) valve were identified. Five neonates had severe systemic AV valve regurgitation with severe coarctation of the aorta (n = 4) or aortic atresia (n = 1) and presented with heart failure. Four died in the neonatal period and one who had coarctation repair died 7 months postoperatively. The remaining five patients with congenitally corrected transposition and Ebstein's anomaly had mild left AV valve regurgitation; none of these had aortic arch obstruction. In neonates who have coexisting Ebstein's anomaly of the systemic AV valve and congenitally corrected transposition, obstruction to aortic arch flow is common. Severe systemic AV valve regurgitation with a morphologic systemic right ventricle may have contributed to low anterograde flow in the ascending aorta prenatally and thereby to the aortic arch abnormality.