Background/aim: Obstructive sleep apnea syndrome (OSAS) is a disease characterized by episodic hypoxia. We aimed to use the Freesurfer program for global evaluation of morphological changes in OSAS patients. Materials and methods: Three-dimensional T1-weighted images were obtained, and intracranial morphology was assessed in 18 patients with OSAS and 20 controls. Results of the volume and the cortical thickness analyses of both groups were compared statistically. Results: The total cortical, left-right hemispheres gray matter (GM), corpus callosum, and total GM volumes were lower in OSAS patients when compared with the control group (P < 0.001). The average cortical thickness was lower in OSAS patients bilaterally in pars orbitalis, paracentral, rostral middle frontal, middle frontal, orbital, and superior frontal gyri when compared with the control group (P < 0.05). Furthermore, the volume and average cortical thickness of multiple anatomic regions, apart from the brain parts mentioned above, were decreased unilaterally (e.g., hippocampus, cingulum, putamen, thalamus) in OSAS patients (P < 0.05). Conclusion: Multiple morphologic changes occur in the cerebral structures of OSAS patients due to intermittent ischemia episodes. Detection of those areas with Freesurfer is easier. New studies with large series would be needed for these subjects.