The purpose of this study was to investigate whether the origins and courses of the coronary arteries could be better assessed using ECG-gated dual-source computed tomography (CT) than with echocardiography in neonates with transposition of the great arteries (TGA). A total of 17 neonates within 14days old who underwent both echocardiography and retrospective ECG-gated coronary CT angiography were retrospectively reviewed. The patients were sedated and intubated during CT examinations, and CT images were obtained with a breath-hold. CT images were reconstructed by multiple cardiac phases, and the coronary artery assessment was performed in the most static phase. Coronary anomalies were classified by Shaher's classification and validated by surgical findings. CT correctly classified 16 of 17 cases (Shaher type 1: 7, type 2: 4, type 9: 3, type 3: 1, type 4: 2), whereas echocardiography classified only 8 of 17 cases correctly. Dual-source CT had a significantly higher diagnostic ability than echocardiography (p = 0.0078). Dual-source coronary CT angiography has a higher diagnostic ability than echocardiography in the assessment of the origins and courses of the coronary arteries in neonates with TGA.