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The study of the causes of transsexuality investigates gender identity formation of transgender people, especially those who are transsexual. Transgender people have a gender identity that does not match their assigned sex, often resulting in gender dysphoria. The causes of transsexuality have been studied for decades. The most studied factors are biological, especially brain structure differences in relation to biology and sexual orientation. Environmental factors have also been proposed.

Transgender brain studies, especially those on trans women who are sexually attracted to women (gynephilic), and those on trans men who are sexually attracted to men (androphilic), are limited, as they include a small number of tested individuals. The available research indicates that the brain structure of androphilic trans women with early-onset gender dysphoria is closer to the brain structure of cisgender women's and less like cisgender men's. It also reports that both androphilic trans women and trans women with late-onset gender dysphoria who are gynephilic have different brain phenotypes, and that gynephilic trans women differ from both cisgender male and female controls in non-dimorphic brain areas. Cortical thickness, which is generally thicker in cisgender women's brains than in cisgender men's brains, may also be thicker in trans women's brains, but is present in a different location to cisgender women's brains. For trans men, research indicates that those with early-onset gender dysphoria and who are gynephilic have brains that generally correspond to their assigned sex, but that they have their own phenotype with respect to cortical thickness, subcortical structures, and white matter microstructure, especially in the right hemisphere. Hormone use can also affect transgender people's brain structure; it can cause transgender women's brains to become closer to those of cisgender women, and morphological increments observed in the brains of trans men might be due to the anabolic effects of testosterone.

Twin studies suggest that there are likely genetic causes of transsexuality, although the precise genes involved are not fully understood. One study published in the International Journal of Transgender Health found that 33% of identical twin pairs were both trans, compared to only 2.6% of non-identical twins who were raised in the same family at the same time, but were not genetically identical.

Ray Blanchard created a taxonomy of male-to-female transsexualism that proposes two distinct etiologies for androphilic and gynephilic individuals that has become controversial, supported by J. Michael Bailey, Anne Lawrence, James Cantor and others, but opposed by Charles Allen Moser, Julia Serano, and the World Professional Association for Transgender Health.

Biological factors