There are limited data regarding the influence of commissural malalignment of the aortic-pulmonary sinus on the arterial switch operation. To compare diagnostic accuracy between cardiac CT and echocardiography for evaluating commissural malalignment of aortic-pulmonary sinus in children with complete transposition of the great arteries and to seek potential clinical implication of commissural malalignment on the arterial switch operation. In 37 patients (35 boys; median age: 8 days, range: 3-80 days) with complete transposition of the great arteries who had tricuspid semilunar valves and underwent an arterial switch operation, the degree of the commissural rotation of the aortic-pulmonary sinus was assessed on cardiac CT (n=37) and echocardiography (n=35). With surgical finding as a reference, cardiac CT was compared with echocardiography in identifying commissural malalignment in 35 patients. The influence of the height difference between the semilunar valves measured by cardiac CT on the identification of commissural malalignment with cardiac CT and echocardiography was evaluated. The impact of commissural malalignment on coronary transfer techniques was evaluated. In operative findings, the commissures of the semilunar valves were aligned in 24 patients and malaligned in 13. With surgical findings as a reference, cardiac CT showed higher, but not statistically significant (P >0.05), sensitivity (91.7% vs. 75.0%), specificity (87.0% vs. 78.3%) and accuracy (88.6% vs. 77.1%) for the diagnosis of the malalignment than echocardiography. The measured height difference between the semilunar valves did not affect the identification of the malalignment with cardiac CT and echocardiography. The surgical malalignment group showed a higher requirement of modified coronary transfer techniques than the surgical aligned group (11/13 vs. 11/24, P=0.03). Cardiac CT and echocardiography appear useful for evaluating commissural malalignment of the semilunar valves in patients with complete transposition of the great arteries frequently requiring modified coronary transfer techniques at during an arterial switch operation.