White matter injury (WMI) is a known complication following neonatal heart surgery in term infants. In preterm infants, WMI has been associated with the degree of systemic inflammation. It is not known whether inflammation is an important mechanism of WMI as documented by magnetic resonance imaging (MRI) following neonatal heart surgery with cardiopulmonary bypass. Term neonates with congenital heart disease were enrolled in a prospective study with postoperative MRI. White matter injury was recorded by the number of T1 hyperintense foci with >5 foci consistent with significant WMI. Eleven candidate cytokine markers (INF-gamma, TNF-alpha, IL-1 beta, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, and IL-13) were assayed preoperatively and daily for 5 days following surgery. Multiple clinical factors were recorded and correlated with WMI. Ninety-two subjects were enrolled in the study. The median age at surgery was 5 days (interquartile range 4–7 days). Compared with the presurgery level, there were statistically significant increases (p < 0.005) for 8 out of 11 inflammatory markers. In all, 64 postoperative MRIs were performed. No significant correlation was detected between WMI and clinical variables or inflammatory markers assessed immediately postoperative and on postoperative days 1 and 3, with exception of IL-1 beta on postoperative day 1. WMI correlates poorly with the systemic inflammatory response after congenital heart surgery and a number of herein measured clinical factors. WMI following neonatal heart surgery is a complex, still incompletely understood phenomenon that warrants continued investigation.