Congenital persistence of the fifth aortic arch is an unusual, often misdiagnosed and underestimated pathological finding. It is usually associated with other cardiac or vascular anomalies, which makes every case quite unique in its clinical presentation and treatment. Our subject was a newborn (1-month-old male) who was referred to our hospital from a peripheral centre owing to difficulty in obtaining a clear diagnosis with traditional means (echocardiography). He presented with Type II left-sided malformation (atresia or interruption of the superior arch with patent inferior arch) and also showed an associated atrial septal defect with left-to-right-shunt. The investigation was carried out with a contrast-enhanced CT scan owing to the serious clinical condition (haemodynamic instability) of the subject that made an MRI examination too hazardous. The study succeeded in plainly depicting the malformation, providing a clear diagnosis and also giving the surgeons (especially with the assistance of three-dimensional volume rendering reconstruction) an accurate anatomical model, which played a crucial role in planning the operation. The ability of a multislice CT scan to rapidly perform a full, panoramic and minimally invasive study of the cardiovascular system is clearly demonstrated in this study. The only downside of this procedure is the use of ionizing radiation on a newborn, although it is justified in this case by the emergent need for a quick diagnosis. Furthermore, a CT scan is characterized by a higher spatial resolution compared with an MRI and for vascular anomalies, a CT scan is often preferred. An MRI is mainly used in case of functional imaging. Exactly for this reason, we planned the procedure in order to maintain the equivalent radiation dose as low as possible [equivalent dose (H) ≤ 1 mSV].