Brain and heart development occur simultaneously in the human fetus. Given the depth and complexity of these shared morphogenetic programs, it is perhaps not surprising that disruption of organogenesis in one organ will impact the development of the other. Newborns with congenital heart disease show a high frequency of acquired focal brain injury on sensitive magnetic resonance imaging studies in the perioperative period. The surprisingly high incidence of white matter injury in these term newborns suggests a unique vulnerability and may be related to a delay in brain development. These abnormalities in brain development identified with MRI in newborns with congenital heart disease might reflect abnormalities in cerebral blood flow while in utero. A complete understanding of the mechanisms of white matter injury in the term newborn with congenital heart disease will require further investigation of the timing, extent, and causes of delayed fetal brain development in the presence of congenital heart disease.