Suicide is a serious public health problem, but little is known of microstructural abnormalities of white matter regarding suicidal ideation (SI). Sixteen depressive patients with SI, 16 depressive patients without SI and 32 age- and gender-matched healthy controls received MRI scans on a 3T magnet. Whole-brain voxel-based analysis was used to compare fractional anisotropy (FA) across the three groups with threshold at p<0.005(uncorrected) at voxel level and 50 for cluster size with SPM8. The three groups had significant differences of FA in the left centrum semiovale (peak Z=4.64 at -30, -38, 34), right centrum semiovale (peak Z=3.54 at 32, -34, 32) and right splenium of corpus callosum (peak Z=4.64 at 4, -34, 12). The alterations of white matter tract indicate that white matter integrity, especially a “frontal-related WM disconnection” may underlie the pathophysiology of suicidal ideation in depression.