Significance: Studying individual differences in gender and sexual orientation provides insight into how early-life biology shapes brain and behavior. The literature identifies multiple biodevelopmental influences on male sexual orientation, but these influences are generally studied individually, and the potential for association or interaction between them remains largely unexplored. We hypothesized that distinct biodevelopmental pathways correspond to specific subgroups of nonheterosexual men. We present evidence that nonheterosexual men can be categorized into at least four subgroups based on established biomarkers, and these biodevelopmental pathways differentially relate to gender expression and personality traits. These findings indicate individual differences in biodevelopmental pathways of male sexual orientation. They also illustrate the value of latent profile analyses for studying individual differences.