Obstructive sleep apnea is associated with abnormalities in neuropsychologic function, and defects in respiratory control may contribute to pathogenesis. Abnormalities may be reflected in structural brain changes. Twenty-seven male untreated patients with severe sleep apnea without comorbidities, and 24 age-matched control subjects, had T1-weighted brain imaging in a high-resolution magnetic resonance scanner. Twenty-three patients with sleep apnea had repeat imaging after 6 months of continuous positive airways pressure treatment. No areas of gray matter volume change were found in patients using an optimized voxel-based morphometry technique, at p < 0.05 adjusted for multiple comparisons (despite the method being sensitive to changes in gray matter fraction of 0.17 or less in all voxels). Furthermore, no differences were seen in bilateral hippocampal, temporal lobe, or whole brain volumes, assessed by manual tracing of anatomical borders. No longitudinal changes were seen in gray matter density or regional volumes after treatment, but whole brain volume decreased slightly. We have found no gray matter volume deficits nor focal structural changes in severe obstructive sleep apnea. Whole brain volume decreases without focal changes after 6 months of continuous positive airways pressure treatment.