MRI scans of patients with idiopathic generalized epilepsy (IGE) are normal on visual assessment. Using an interactive anatomical segmentation technique and volume-of-interest measurements of MRI, we showed recently that patients with IGE had significantly larger cortical grey matter than control subjects. Further, 40% of individual patients with juvenile myoclonic epilepsy (JME), a syndrome of IGE in adolescence, had significant abnormalities of cerebral structure. In this study, we applied the automated and objective technique of statistical parametric mapping (SPM) to the analysis of structural MRI from 20 patients with JME and 30 control subjects. The cortical grey matter of each individual JME patient and the group of JME patients was contrasted with that of the group of 30 normal subjects. The voxel-based SPM comparison between the group of JME patients and the control subjects showed an increase in cortical grey matter in the mesial frontal lobes of the patients. Analysis of individual patients revealed significant abnormalities of cortical grey matter in five out of 20 JME patients, four of whom had been shown to have widespread abnormalities using the previous volume of interest technique. These findings indicate a structural cerebral abnormality in JME, with involvement of mesiofrontal cortical structures.