If humans are exposed prenatally to antiepileptic drugs (AEDs), cognitive impairment may be the consequence. Driven by results of experimental work showing that AEDs may induce neuronal death in the developing rodent brain, we wanted to explore whether prenatal exposure to AEDs (PAE) may result in structural changes in the human brain. For this purpose we investigated a group of healthy young adults with PAE and a group of age-matched unexposed healthy controls by magnetic resonance imaging (MRI) of the brain. Local differences in cerebral morphology associated with PAE were analysed in volumetric MRI data by use of voxelwise comparisons of grey and white matter images. Significant regional decreases of grey matter volumes were found in PAE subjects in the area of the lentiform nucleus, including both pallidum and putamen bilaterally, and the hypothalamus. No significant regional differences in white matter volumes were found. We conclude that PAE causes subtle morphological changes in grey matter of the human brain which are conform with lower cell numbers in the basal ganglia and the hypothalamus.