Background: Sex differences in brain morphology have been extensively investigated up to today, demonstrating that biological sex differences are linked to a number of brain structures. Sexual orientation (hetero- versus homosexuality) has been found to be associated with differences in the functioning of subcortical brain regions such as the thalamus, hypothalamus, parahippocampus and septal area. However, there is currently little research on morphological brain changes associated with sexual orientation.Methods: The total sample comprised 74 participants, 37 men (21 homosexual) and 37 women (19 homosexual). Sexual orientation was assessed via self-report. High resolution anatomical images of the participants were analyzed by means of voxel-based morphometry in whole-brain analyses using the Computational Anatomy Toolbox (CAT12). Grey matter volumes (GMV) were compared with respect to sexual orientation across the whole sample and by biological sex using full factorial designs controlling for age, total intracranial volume, education and handedness. A family-wise error correction (p < 0.05) at the voxel level was applied to correct for multiple comparisons.Results: Irrespective of biological sex, hetero- versus homosexual participants exhibited more GMV in the thalamus and precentral gyrus. Sex-specific analysis revealed that hetero- compared to homosexual females had increased GMV specifically in the precentral gyrus, whereas hetero- versus homosexual males exhibited more GMV in the thalamus.Conclusion: Our results indicate that sexual orientation has unique effects on brain structure and that these effects between the sexes. These findings provide important new insights into the brain morphology underlying sexual orientation.