Background Earlier studies found that gray matter volume in the frontal, parietal and temporal lobes is significantly altered in idiopathic generalized epilepsy (IGE).Research has indicated that a relationship exists between the brains subcortical structures and epilepsy.However, little is known about possible changes in the subcortical structures in IGE.Objective To determine the changes in the shape of subcortical structures in IGE using vertex analysis.Methods Fourteen male patients with IGE and 28 age-and sex-matched healthy controls were included in this study, which used high-resolution magnetic resonance imaging.We performed a vertex-based shape analysis, in which we compared patients with IGE with the controls, on the subcortical structures that we had obtained from the MRI data.Results Statistical analysis showed significant regional atrophy in the left thalamus, left putamen and bilateral globus pallidus in patients with IGE.Conclusion These results indicate that regional atrophy of the basal ganglia and the thalamus may be related to seizure disorder.In the future, these findings may prove useful for choosing new therapeutic regimens.