Objective To observe cortial activation areas in comitant strabismus patients in response to different disparity stereogram stimuli and to compare average activation voxels in comitant strabismus patients and normal subjects. Methods This was a case series study. Twelve subjects （mean age 16.9±3.9 years） with comitant strabismus and 10 healthy volunteers （mean age 21.2±2.7 years） were enrolled. The experiment was a block design. Three uncrossed disparity （1 200″， 2 400″ and 3 600″） random-dot stereograms （RDS） were presented during the on-stimulus phase， and a black cross line fixed in the center of a white screen was displayed during the off- stimulus phase. Functional MRI data were processed with the statistical parametric mapping 5 software and t test. Results During the disparity of 1 200″ RDS stimulus， the right inferior occipital gyrus and left middle occipital gyrus （BA18） showed activation in the healthy group， and the left middle occipital gyrus （BA18） showed activation in the strabismus group. During the disparity of 2 400″ RDS stimulus， and bilateral middle occipital gyruses （BA18） and the right inferior temporal gyrus （BA37） showed activation in the healthy group， and bilateral middle occipital gyruses （BA18） showed activation in the strabismus group. During the disparity of 3 600″ RDS stimulus， bilateral middle occipital gyruses （BA18） showed activation in the healthy group， but no significant activation area was observed in the strabismus group. Under three different disparity stimuli， the average activation voxels in the comitant strabismus group were significantly lower than in the healthy group （t=-3.16， -3.38， -2.47， P<0.05）. Conclusion During RDS stimuli， bilateral occipital lobes showed activation in comitant strabismus and normal subjects. In addition， the right temporal lobe showed activation in the healthy subjects. Under different disparity stimuli， average activation voxels in comitant strabismus patients are lower than in healthy subjects.