Brain injury is a frequent complication in newborns with complex congenital heart disease (CHD) secondary to hemodynamic instability and increased risk for hypoxic-ischemic injury. In this study quantitative susceptibility mapping (QSM) was performed in newborns with complex CHD prior to open heart surgery and was compared to healthy control newborns. Mean susceptibility was significantly higher in the cortical gray matter of neonates with CHD versus controls suggesting reduced oxygenation in the cerebral vasculature in CHD preoperatively. QSM images also depicted less contrast in the CHD, which may be associated with delayed brain development. This is the first report to demonstrate the feasibility of neonatal QSM and susceptibility differences between CHD and controls.