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Exploration of the relationships between regional brain volume and anxiety-related personality traits is important for understanding preexisting vulnerability to depressive and anxiety disorders. However, previous studies on this topic have employed relatively limited sample sizes and/or image processing methodology, and they have not clarified possible gender differences. In the present study, 183 (male/female: 117/66) right-handed healthy individuals in the third and fourth decades of life underwent structural magnetic resonance imaging scans and Temperament and Character Inventory. Neuroanatomical correlates of individual differences in the score of harm avoidance (HA) were examined throughout the entire brain using voxel-based morphometry. We found that higher scores on HA were associated with smaller regional gray matter volume in the right hippocampus, which was common to both genders. In contrast, female-specific correlation was found between higher anxiety-related personality traits and smaller regional brain volume in the left anterior prefrontal cortex. The present findings suggest that smaller right hippocampal volume underlies the basis for higher anxiety-related traits common to both genders, whereas anterior prefrontal volume contributes only in females. The results may have implications for why susceptibility to stress-related disorders such as anxiety disorders and depression shows gender and/or individual differences.