Neonates with severe CHD require CPB within the first days of life. White matter injury can occur before surgery, and this may impair the long-term neurodevelopmental and psychosocial outcome. The purpose of this study was to assess the microstructural development of the CC in infants with CHD before and after CPB for transposition of the great arteries. Fifteen patients with CHD and 11 age-matched HC were recruited. We separately quantified the parallel (E1) and perpendicular (E23) diffusions, the ADC, and FA of the genu of the CC and splenium of the CC before and after surgery. In presurgical measures of the genu of the CC, higher E23 (P = .018), higher ADC (P = .026), and lower FA (P = .033) values were measured compared with those in HC. In the postsurgery scans, the genu of the CC had higher E23 (P = .013), higher ADC (P = .012), and lower FA (P = .033) values compared with those in HC. There was no significant difference in any DTI indices between the pre- and postsurgical groups. We report abnormal microstructural development in the genu of the CC of infants with d-TGA before and after CPB. High E23, high ADC, and low FA values in the genu of the CC may be explained by abnormal axonal pruning, thinner myelin sheaths, smaller axonal diameters, or more oligodendrocytes. It appears that the genu of the CC is more vulnerable than the splenium of the CC in patients with CHD and may serve as a biomarker to identify infants at highest risk for adverse neurodevelopmental outcome.