Narcissistic traits have been linked to structural and functional brain networks, including the insular cortex, however, with inconsistent findings. In this study, we tested the hypothesis that subclinical narcissism is associated with variations in regional brain volumes in insular and prefrontal areas. We studied 103 clinically healthy subjects, who were assessed for narcissistic traits using the Narcissistic Personality Inventory (NPI, 40-item version) and received high-resolution structural magnetic resonance imaging. Voxel-based morphometry was used to analyse MRI scans and multiple regression models were used for statistical analysis, with threshold-free cluster enhancement (TFCE). We found significant (p < 0.05, family-wise error FWE corrected) positive correlations of NPI scores with grey matter in multiple prefrontal cortical areas (including the medial and ventromedial, anterior/rostral dorsolateral prefrontal and orbitofrontal cortices, subgenual and mid-anterior cingulate cortices, insula, and bilateral caudate nuclei). We did not observe reliable links to particular facets of NPI-narcissism. Our findings provide novel evidence for an association of narcissistic traits with variations in prefrontal and insular brain structure, which also overlap with previous functional studies of narcissism-related phenotypes including self-enhancement and social dominance. However, further studies are needed to clarify differential associations to entitlement vs. vulnerable facets of narcissism.