Heterogeneity in brain morphology and psychological, cognitive, and contextual factors of gender identity

Once understood in binary terms, gender identity is increasingly recognized as a multidimensional and continuous construct shaped by both sociocultural and neurobiological factors. Although prior studies have reported associations between gender identity and brain structure, few have adopted an integrative approach to examine how gender identity emerges. Drawing on a large, non-clinical sample of young adults from the Amsterdam Open Magnetic Resonance Imaging Collection (n = 544), this study integrated psychological assessments, socioeconomic indicators, and structural MRI to investigate the relationship between gender identity and brain morphology. For participants assigned female at birth, a feminine identity was linked to reduced cortical thickness in several brain regions, including the parahippocampal, fusiform, lingual, and pericalcarine cortices. Among these regions, two distinct pathways related to the fusiform cortex were identified: a self-referential pathway (through the parahippocampal cortex) and a visual-perceptual pathway (through the pericalcarine and lingual cortices). Besides, an additional pathway related to the fusiform cortex was also identified, which connected higher socioeconomic status to crystallized intelligence. For participants assigned male at birth, a feminine identity was associated with increased anxiety and reduced cortical thickness in visual-emotional regions. In contrast, masculine identity was linked to a larger cortical area in the supramarginal gyrus and insula. Altogether, these findings suggest that gender identity is embedded in distributed neural systems that support self-representation, and that its structural correlates emerge through distinct psychological and cognitive-contextual mechanisms. By moving beyond binary classification, this study may offer a more nuanced neurobiological model of gendered self-concept in the general population.