High-resolution MRI of the brain has made it possible to identify focal cortical dysplasia (FCD) in an increasing number of patients. There is evidence for structural abnormalities extending beyond the visually identified FCD lesion. Voxel-based morphometry (VBM) has the potential of detecting both lesions and extra-lesional abnormalities because it performs a whole brain voxel-wise comparison. However, on T1-weighted MRI, FCD lesions are characterized by a wide spectrum of signal hyperintensity that may compromise the results of the segmentation step in VBM. Our purpose was to investigate gray matter (GM) changes in individual FCD patients using voxel-based morphometry (VBM). In addition, we sought to assess the performance of this technique for FCD detection with respect to lesion intensity using an operator designed to emphasize areas of hyperintense T1 signal. We studied 27 patients with known FCD and focal epilepsy and 39 healthy controls. We compared the GM map of each subject (controls and patients) with the average GM map of all controls and obtained a GM z-score map for each individual. The protocol being designed to achieve a maximal specificity, no differences in GM concentration were found in the control group. The z-score maps showed an increase in GM that coincided with the lesion in 21/27 (78%) patients. Five of the six remaining patients whose lesions were not detected by VBM presented with a strong lesion hyperintensity, and a significant part of their lesion was misclassified as white matter. In 16/27 (59%) patients, there were additional areas of GM increase distant from the primary lesion. Areas of GM decrease were found in 8/27 (30%) patients. In conclusion, individual voxel-based analysis was able to detect FCD in a majority of patients. Moreover, FCD was often associated with widespread GM changes extending beyond the visible lesion. In its current form, however, individual VBM may be unable to detect lesions characterized by strong signal intensity abnormalities.