To compare the difference in white matter volume (WMV) and gray matter volume (GMV) between the comitant strabismus (CS) patients and health controls by voxel-based morphometry (VBM) and the relationship with behavioral performance. A total of 20 patients with comitant strabismus (10 males and 10 females), and 20 healthy subjects (10 males and 10 females) with matched age, sex status underwent magnetic resonance examination. The authors analyzed the original 3D T1 brain images using the VBM module. The comitant strabismus groups were compared with the control groups for the GMW and WMV of the entire brain. Correlation analysis was performed to investigate the relationship between the GMV and WMV altered areas and the behavioral performance in comitant strabismus. CS patients were distinguishable from the healthy controls (HCs) by receiver operating characteristic curves. Results of the VBM analysis demonstrated that the CS groups had decreased GMV in the brain regions of the left middle temporal pole, left cerebellum posterior lobe, right posterior cingulate cortex, left cuneus and right premotor cortex. Meanwhile, the WMV was significantly decreased in the brain regions of the left middle temporal gyrus, right middle temporal gyrus, left middle temporal gyrus, right precuneus and right premotor cortex in the comitant strabismus patients compared with HCs. Furthermore, the duration of CS was negatively correlated with the GMV values of the left middle temporal pole (r=−0.486, P=0.030). CS caused GMV and WMV atrophy in many brain regions, which may indicate the neural mechanisms of the ocular motility disorders in CS patients.