BACKGROUND AND PURPOSE: Voxel-based morphometry is widely used for detecting gray matter abnormalities in epilepsy. However, its performance with changing parameters, smoothing and statistical threshold, is debatable. More important, the potential yield of combining multiple MR imaging contrasts (multispectral voxel-based morphometry) is still unclear. Our aim was to objectify smoothing and statistical cutoffs and systematically compare the performance of multispectral voxel-based morphometry with existing T1 voxelbased morphometry in patients with focal epilepsy and previously negative MRI. MATERIALS AND METHODS: 3D T1-, T2-, and T2-weighted FLAIR scans were acquired for 62 healthy volunteers and 13 patients with MR imaging negative for focal epilepsy on a Magnetom Skyra 3T scanner with an isotropic resolution of 0.9 mm 3. We systematically optimized the main voxel-based morphometry parameters, smoothing level and statistical cutoff, with T1 voxel-based morphometry as a reference. As a next step, the performance of multispectral voxel-based morphometry models, T1ϩT2, T1ϩFLAIR, and T1ϩT2ϩFLAIR, was compared with that of T1 voxel-based morphometry using gray matter concentration and gray matter volume analysis. RESULTS: We found the best performance of T1 at 12 mm and a T-threshold (statistical cutoff) of 3.7 for gray matter concentration analysis. When we incorporated these parameters, after expert visual interpretation of concordant and discordant findings, we identified T1ϩFLAIR as the best model with a concordant rate of 46.2% and a concordant rate/discordant rate of 1.20 compared with T1 with 30.8% and 0.67, respectively. Visual interpretation of voxel-based morphometry findings decreased concordant rates from 38.5%-46.2% to 15.4%-46.2% and discordant rates from 53.8%-84.6% to 30.8%-46.2% and increased specificity across models from 33.9%-40.3% to 46.8%-54.8%. CONCLUSIONS: Multispectral voxel-based morphometry, especially T1ϩFLAIR, can yield superior results over single-channel T1 in focal epilepsy patients with a negative conventional MR imaging. ABBREVIATIONS: AUC ϭ area under the curve; C R ϭ concordant rate; D R ϭ discordant rate; EEG ϭ electroencephalography; GMC ϭ gray matter concentration; GMV ϭ gray matter volume; S P ϭ specificity; VBM ϭ voxel-based morphometry