© The Author(s), 2022. Published by Cambridge University PressAbstract Background: The effect of prenatal diagnosis on prognosis in patients with transposition of the great arteries is not clear. In this study, we compared the outcomes after arterial switch operation. Methods: Outcome of 112 patients who had arterial switch operation in the neonatal period were analysed. The patients were divided into two groups: those who had prenatal diagnosis (Group 1; n = 34) and those who did not (Group 2; n = 78). The patients were also classified based on their diagnosis: simple transposition, transposition with ventricular septal defect and/or aortic arch hypoplasia, and Taussig–Bing anomaly. Results: In Group 1, the C-section delivery rate was higher (82% vs. 44%; p = 0.004), and it was observed that patients in Group 1 were more often intubated upon admission to the neonatal ICU (38% vs. 9%; p = 0.005). No differences were found between the two groups in terms of operation time, cardiopulmonary bypass time, post-operative invasive respiratory support duration, or extracorporeal membrane oxygenation support. It was observed that those who had Taussig–Bing anomaly had a higher mortality. Conclusions: Timely treatment have a positive effect on neonatal mortality and morbidity. That’s why all families with prenatal diagnosis of critical CHD should be recommended to have the delivery in a tertiary care hospital. Although it could not be demonstrated in this study, prenatal diagnosis has a potential to improve surgical results especially in countries or cities, which does not have enough resources for transfer and surgical units. Further efforts are needed to improve prenatal screening programmes.