Advances in neuroimaging have enabled studies of specific neuroanatomical abnormalities with relevance to schizophrenia. This study quantified structural alterations on brain magnetic resonance (MR) images of patients with schizophrenia. MR brain imaging was done on 88 control and 57 schizophrenic subjects and Dicom images were analyzed with ImageJ software. The brain volume was estimated with the planimetric stereological technique. The volume fraction of brain structures was also estimated. The results showed that, the mean volume of right, left, and total hemispheres in controls were 551, 550, and 1101 cm³, respectively. The mean volumes of right, left, and total hemispheres in schizophrenics were 513, 512, and 1026 cm³, respectively. The schizophrenics’ brains were smaller than the controls (p < 0.05). The mean volume of total white matter of controls (516 cm³) was bigger than the schizophrenics’ volume (451 cm³), (p < 0.05). The volume fraction of total white matter was also lower in schizophrenics (p < 0.05). Volume fraction of the lateral ventricles was higher in schizophrenics (p < 0.05). According to the findings, the volumes of schizophrenics’ brain were smaller than the controls and the volume fractional changes in schizophrenics showed sex dependent differences. We conclude that stereological analysis of MR brain images is useful for quantifying schizophrenia related structural changes.