The diagnostic and prognostic value of magnetic resonance imaging in the tuberous sclerosis complex has increasingly been recognized. In this paper, we review the presumed pathogenesis of the cerebral dysgenesis seen in this condition in the light of magnetic resonance imaging features of selected patients. In addition to typical findings related to tubers, we show and discuss varied cortical malformations (from simple localized cortical dysplasia to transmantle dysplasia and schizencephaly) similar to those seen in sporadic cerebral dysgenesis. These cases support the hypothesis that the tuberous sclerosis complex focally affects the radial glial-neuronal complex as a basic unit for brain development. Abnormal stem cells would create dysplastic glia and neurons that fail to differentiate, proliferate, migrate and form a normally organized cortex.