We report the unusual finding of brain malformations in a male newborn with anomalies of VACTERL association. Magnetic resonance imaging revealed hypoplasia of cerebellum, pons and corpus callosum as well as kinking of diencephalon and mesencephalon. These malformations of ectodermal tissue are suggestive of a defect of morphogenesis that occurred earlier than usually postulated for VACTERL cases. They resulted in severe neurologic complications and an early death. The fact that a cousin of this patient has VACTERL anomalies without cerebral involvement indicates that variable expressivity in genetically predisposed individuals may be possible for this subgroup of VACTERL cases.