Background & Aim: Congenital heart disease (CHD) is the most frequent congenital malformations. Children with CHD remain at risk of neurodevelopmental impairment, characterized by mild cognitive impairment, impaired social and communication skills, inattention and later, deficits in executive function.This study aimed to characterize brain lesions using MRI in CHD either cyanotic or acyanotic to assess which lesions are associated more with brain injury. Methods: This study was conducted on 30 infants with CHD from the cardiology clinic and general ward at Benha University Hospitals. Patients were subjected to full history taking, complete clinical assessment and investigations as X-ray, Echocardiography and MRI brain. Results: In our study, 20% of CHD infants had brain injury on MRI assessment. The most frequent brain injury was arterial ischemic stroke (20%), followed by white matter injury (6.7%), cerebellar hypoplasia (3.3%), and hypoxic injury (3.3%). There was a statistically significant difference between cyanotic and acyanotic heart diseases regarding brain lesion. There was no statistically significant difference in brain lesion regarding type of cardiac lesion. Conclusion: MRI provides a good screening method in the detection of brain lesions in infants with CHD, helping to improve the cognitive functions and skills in these patients.