In the normal adult human brain, there are quantitative relationships between a surface area measure of the grey matter and the volume of hemispheric grey matter, the volume of the hemispheric subcortical matter and the cross-sectional area of the corpus callosum as revealed by analysis of high resolution MRI data. These relationships reflect structural order in, and biological features of, normal human cerebral hemispheres. Cerebral dysgenesis (CD) is associated with disruption of the normal organization of the hemispheres to a greater or lesser extent and is often manifest as refractory epilepsy. We have examined structural proportions and their disruption in the brains of patients with epilepsy and CD. We found that structural measures were abnormal in 60% of patients with CD, with abnormalities in 64% of hemispheres that, on visual inspection alone, appeared completely normal. We showed that the disruptions found are compatible with expected histopathology in cases where histopathology may be predictable, and that extensive abnormalities may be due to abnormal patterns of connections within the hemispheres. In some cases, it may be possible to predict histopathology on the basis of quantitative analyses of high resolution MRI data, when such prediction is not possible on visual inspection alone.