In patients with idiopathic generalized epilepsy (IGE), visual inspection of routine MRI is normal. However, pathological studies have shown microdysgenesis in grey and white matter in a large percentage of autopsies from cases of IGE. Recently, widespread structural changes not evident on visual inspection of high resolution MRI have been shown using quantitative MRI in patients with apparently focal cerebral dysgenesis. We sought to determine whether similar quantitative changes might be present in patients with IGE, reflecting possible underlying structural abnormalities. Twenty patients with juvenile myoclonic epilepsy, 10 patients each with childhood absence epilepsy and juvenile absence epilepsy, five patients with tonic-clonic seizures on awakening and 30 control subjects had T1-weighted volume acquisition MRI scans on a 1.5T GE scanner. The cerebral hemispheres were segmented semi-automatically, allowing the comparison of normalized cortical and subcortical matter volumes between groups, and investigation of the regional distribution of cortical and subcortical matter in individual subjects. Patients with IGE had significantly larger cortical grey matter volumes than control subjects. Significant abnormalities of the regional distribution of cerebral grey and subcortical matter were found in eight out of 20 patients with juvenile myoclonic epilepsy, one out of 10 patients with childhood absence epilepsy, four out of 10 patients with juvenile absence epilepsy and two out of five patients with tonic-clonic seizures on awakening, but in none of the 30 control subjects. Using MRI-segmentation, we identified widespread cerebral structural changes in patients with various IGE syndromes. Quantitative MRI supports the existence of structural abnormalities in patients with IGE.