Histopathologic evaluation of brain tissue derived from surgically treated patients with medically refractory temporal lobe epilepsy (TLE) frequently reveals structural brain lesions in the surgical specimen. While several of the most commonly encountered lesions such as low-grade neoplasms or vascular malformations are well established as structural substrates of epilepsy, the significance of subtle microscopic characteristics has remained controversial. Within the spectrum a broad range of microscopic features has previously been reported as "mild cortical dysplasia," "focal cortical dysplasia," or "microdysgenesis," including cortical laminar disorganization, columnar arrangement of cortical neurons, marked clustering of neurons throughout cortical layers II-VI, increased numbers of molecular layer neurons, marked perivascular clustering of oligodendroglia in the white matter, single heterotopic neurons in the deep white matter, glioneuronal hamartia, giant neurons, and balloon cell change. In this paper we report the frequency of these features in temporal lobe tissue of 47 surgically treated TLE-patients vs 29 normal autopsy controls. While most of them were found in both cases and controls, clustering of neurons throughout cortical layers II-VI, perivascular clustering of oligodendroglia in the white matter, increased single heterotopic white matter neurons, and glioneuronal hamartias predominated in tissue from patients with epilepsy (p < 0.05). A count of more than 10 white matter neurons/HPF was associated with a worse postoperative outcome (p < 0.05). These data suggest that certain microscopic characteristics are associated with the epileptic process, while others appear as normal variants.