Background. We hypothesized that gender differences in average levels on the internalizing and externalizing factors that account for co-morbidity among common psychopathological syndromes in both men and women account for gender differences in the prevalence of specific syndromes. Method. The latent structure of 11 syndromes was examined in a middle-aged (mean age=52.66 years, s.d.=5.82) sample of 2992 (37% men) members of the community-based Minnesota Twin Registry (MTR) assessed using 10 scales of the Psychiatric Diagnostic Screening Questionnaire (PDSQ) and an adult antisocial behavior scale. Confirmatory factorial invariance models were applied to a best-fitting, internalizing-externalizing model. Results. A 'strong gender invariance model' fit best, indicating that gender differences in the means of individual syndromes were well accounted for by gender differences in mean levels of internalizing and externalizing. Women exhibited higher mean levels of internalizing (d=0.23) and lower mean levels of externalizing (d=-0.52) than men. Conclusions. These findings suggest that risk factors for common mental disorders exhibiting gender differences may influence prevalence at the latent factor level. Future research may benefit from focusing on both the latent factor and individual syndrome levels in explaining gender differences in psychopathology.