Idiopathic trigeminal neuralgia (ITN) is characterized by intermittent, lancinating attacks in the branches of the trigeminal nerve (TGN). 40 ITN patients and 40 matched controls underwent MRI sessions and clinical pain assessment. TGN volume of cisternal segment and whole brain grey matter volume (GMV) were evaluated using voxel-based morphometry, ect. Reduced GMV was found in the insula, dorsal anterior cingulate cortex, precuneus, and several areas of the temporal lobe in ITN subjects. Correlation analysis revealed that decreased GMV of the left insula and decreased TGN volume were associated with increased pain ratings, providing new insight into pathophysiology of the disease.