Microdysgenesis is a microscopic cortical malformation considered to act as a substrate for seizures in some patients with generalized epilepsy. It is also recognized to involve the temporal lobe in a proportion of patients with intractable temporal lobe epilepsy, but the incidence of this abnormality, its relationship to mesial temporal lobe sclerosis and relevance to epileptogenesis remain unknown. This is partly due to a lack of well-defined quantitative pathological diagnostic criteria. To begin to address these issues, we have carried out a rigorous quantitative analysis, using three-dimensional cell counting methods, of several components of microdysgenesis in temporal lobectomy specimens. White matter, cortical and layer I neuronal densities (NDs) were measured using immunohistochemistry for the neuronal markers neuronal nuclear antigen and calbindin D-28-K. Patients with a seizure-free outcome (Class I) showed significantly more microdysgenetic features including higher white matter ND (P < 0.05), particularly of small (<10 microm diameter) neurones (P < 0.01), higher layer I ND (P < 0.05) and increased numbers of Cajal-Retzius-like calbindin-positive neurones (P < 0.05). We also demonstrated that white matter ND was independent of the degree of temporal lobe gliosis as assessed by quantitation of glial fibrillary acidic protein-immunoreactive cells. These findings suggest that microdysgenesis may be a significant lesion in temporal lobe epilepsy in terms of post-surgical prognosis.