The aim of this study was to analyze the brain structures in temporal lobe epilepsy (TLE) using 3D T1-weighed magnetic resonance images (MRI). We used a method of voxel-based morphometry (VBM) with the unified segmentation framework to examine the effects of TLE on specific brain structures in 22 patients. Also, 18 healthy control subjects were included in this study for group comparison. We accomplished GM segmentation, spatial normalization, and intensity non-uniformity correction in the same model. Besides, removal of nonbrain voxels and compensation of spatial normalization effects were performed in this study. Student's t-test statistical models of differences between gray matter concentration (GMC) of patients and controls were obtained using a general linear model (GLM). Compared to controls, TLE presented GMC reduction in hippocampus, amygdala, and entorhinal cortex. Comparison of abnormal areas detected by VBM method and manual delineation of these structures confirms the obtained results.