Objective To investigate the changes of the brain structural connectivity in patients with early-onset schizophrenia (EOS, the onset of psychotic symptoms occurs before 18 years of age).Methods The subjects were 26 patients with EOS and 23 healthy controls (age, sex and years of received education were no significantly different from those of patients). Diffusion weighted images of the whole brains were acquired with a single-shot echo planar imaging (EPI) sequence aligned to the straight axial plane. After preprocessed with DTI-studio and Statistical Parametric Mapping-V (SPM5) software, the fractional anisotropy (FA) images of the two groups underwent two-sample t-test with the methods of voxel-based analysis (VBA) using SPM5 software package. Symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS). Results EOS patients had significantly reduced FA of white matter in the truncus corporis callosi (MNI: 3,16,23; cluser = 1003 voxels) , left temporal lobe (MNI:-28,28,30;cluser = 170 voxels) , left prefrontal lobe (MNI:-28,28,30; cluser = 99 voxels) and right prefrontal lobe (MNI:48,-10,54; cluser =81 voxels) , compared with the healthy controls. Conclusions There is structural disconnectivity of white matter in several brain regions. These abnormal changes may be involved in the neuropathology of schizophrenia.