The objective of this retrospective study was to determine the incidence and types of cranial ultrasound abnormalities in full-term infants with congenital heart disease (CHD). We reviewed the cranial ultrasound scans of 49 full-term infants with CHD and compared them to 42 healthy full-term control infants. The relationship of each abnormality with the type of CHD, the presence of cyanosis, and cardiac catheterization and cardiac surgery were examined. We found that infants with CHD had a higher incidence of cranial ultrasound abnormalities than control infants (59% versus 14%; p < 0.001). Cerebral atrophy and linear echodensities in the basal ganglia and thalamus were the most common sonographic findings in infants with CHD, particularly in those with coarctation of the aorta or ventricular septal defect. Intraventricular hemorrhage occurred more often in infants with acryanotic CHD than in those with cyanotic CHD. Cardiac catheterization and cardiac surgery had no significant effects on cranial ultrasound findings. We conclude that cranial ultrasound abnormalities are very frequent in full-term infants with CHD. These findings emphasize the importance of cranial ultrasonography and long-term neurodevelopmental follow-up of infants with CHD.