<h3>Background</h3> Increasing concerns have been raised about the incidence of perioperative brain injury in neonates with non-cardiac congenital anomalies (NCCA). <h3>Aims</h3> To evaluate brain-injury following neonatal surgery for NCCA using magnetic resonance imaging (MRI). <h3>Methods</h3> Since January 2013 MRI became clinical routine after neonatal surgery for NCCA at our hospital. T1, T2, and DWI were performed to evaluate acute hypoxic-ischaemic injury. Brain injury was assessed on MRI after surgery. <h3>Results</h3> Surgery and MRI were performed respectively at a median postnatal age of 2 days [0–29] and 8 days [3–44] after surgery in 38/45 infants. Thirteen (34%) neonates had a normal MRI-scan (GA 39.0[35.86–40.57], BW 2930, z-score -1.38). Among 14 preterm infants the following lesions (79%) were found: IVH grade II (1), punctate cerebellar haemorrhages (4), punctate white matter lesions (9, PWML) and lenticulostriate-infarction (1). For 24 full-term infants, 58% had brain lesions: punctate cerebellar haemorrhages (2), PWML (5), supra- and infratentorial subdural haemorrhages (mild, 7) and sinus thrombosis (1, superior sagittal sinus). Several infants had a combination of lesions (n = 8). <h3>Conclusion</h3> This cohort shows a wide range of mild to moderate brain lesions in infants with NCCA. Brain injury was more prevalent in preterm infants. Additional research is needed to gain better insight into clinical and surgical risk factors and underlying NCCA, timing of onset and aetiology of brain injury. Neurodevelopmental follow-up should be conducted to evaluate the clinical implications of these findings.