What Science Says About Transgender Identity and the Brain

For years, I have cringed a little when seeing activists holding signs that say “Trans Women are Women.” Not because I don’t believe in my own identity as a transgender woman, but because I wanted to truly understand what the science says. I wanted an answer for when TERFs or gender-critical individuals snidely ask, “What is a woman?” I know that I was born male, but from a young age, I always felt different from other boys and men. This feeling, this deep-seated understanding of myself, pushed me to take a deep dive into the research on the biology of gender identity. What I found was a growing body of scientific evidence that affirms what many of us have always known—gender identity is real, it is biologically rooted, and it is more complex than the binary of male and female.

While biological sex traditionally refers to physical traits like chromosomes, reproductive organs, and hormone levels, gender identity is an individual’s deeply ingrained sense of being male, female, or something entirely else. For most cisgender individuals, gender identity aligns with the sex assigned at birth. However, transgender women (individuals assigned male at birth who identify as female), transgender men (individuals assigned female at birth who identify as male), and non-binary individuals (whose identities do not conform strictly to male or female) experience a misalignment between their gender identity and birth anatomy.

The question of whether transgender individuals are “entirely biologically male or female” is critical, especially in the midst of political and social debates about transgender rights. Anti-trans rhetoric often claims that sex is strictly defined by chromosomes and genitalia, ignoring extensive scientific evidence that brain structure and function play a significant role in gender identity. This article delves into the brain biology of transgender individuals—exploring development from birth through puberty and the effects of hormone replacement therapy (HRT). Using scientific studies as a foundation, we examine the biological underpinnings of gender identity and discuss the broader social and political implications of these findings.

Brain Development in Transgender Women

Decades of research suggest that transgender women’s brains exhibit characteristics distinct from cisgender men and, often, align more closely with cisgender women. A landmark 1995 study examined the bed nucleus of the stria terminalis central subdivision (BSTc), a region of the hypothalamus involved in sexual behavior and identity. Researchers found that transgender women had BSTc sizes and neuron counts comparable to cisgender women rather than cisgender men. Later studies confirmed these findings, demonstrating that transgender women’s BSTc neuron counts were in the female range regardless of whether they had taken HRT.

These differences in brain structure may be a key factor in gender dysphoria, the distress experienced when an individual’s gender identity does not align with their assigned sex at birth. The presence of structural brain differences in sexually dimorphic areas, such as the BSTc, suggests that transgender individuals’ brains develop along a trajectory that diverges from their birth-assigned sex and instead aligns more closely with their experienced gender.

Neuroimaging studies using MRI scans further support this idea. Transgender women’s brain structures and connectivity patterns frequently fall between male and female norms. White matter microstructure, cortical thickness, and brain activation patterns in transgender women before hormone therapy often align more closely with female-typical patterns than male-typical ones. These findings suggest that some aspects of brain development diverge from an individual’s assigned sex at birth, reinforcing the idea that gender identity has neurobiological influences.

Functional brain studies also support this concept. A 2008 study found that transgender women who had not started HRT exhibited female-typical hypothalamic responses to certain pheromone-like odors, a response distinct from cisgender men. Similarly, transgender adolescent girls (assigned male at birth) demonstrated brain activity patterns more similar to cisgender girls than cisgender boys, reinforcing the idea that these neurological differences emerge early in life.

Brain Development in Transgender Men

Research on transgender men (assigned female at birth, but identifying as male) has yielded similar findings. A study using diffusion tensor imaging (DTI) found that transgender men exhibited white matter patterns distinct from cisgender women and more closely aligned with cisgender men. These findings suggest that certain aspects of brain structure in transgender men develop in accordance with their experienced gender.

Additionally, studies have identified differences in subcortical structures that align transgender men more closely with cisgender men. This evidence suggests that brain development in transgender individuals may not strictly adhere to their assigned sex at birth, further challenging the binary understanding of biological sex. As with transgender women, these differences could contribute to gender dysphoria by creating an internal mismatch between the brain’s expectations and the body’s characteristics.

Brain Development in Non-Binary Individuals

While research specifically on non-binary individuals is limited, emerging studies indicate that their brain structures and functional patterns do not always conform to binary male or female norms. A 2020 study on gender-incongruent individuals, including non-binary participants, found unique brain connectivity patterns that differed from both cisgender men and women. This suggests that the neurobiology of gender identity is more diverse than the male-female binary model can explain. More research is needed to fully understand how non-binary identities manifest in brain structure and function. The presence of such neurological patterns could help explain why some individuals do not experience gender in a strictly binary manner.

Changes in Sexual Orientation During HRT

Sexual orientation is a complex interplay of biological, neurological, and social factors. While many people assume that sexual orientation is fixed, scientific research has shown that hormonal changes, particularly those introduced through HRT, can influence patterns of attraction. These changes do not happen to everyone, but they are significant enough to be documented in research.

• A 2014 study found that 32.9% of transgender women and 22.2% of transgender men reported changes in sexual attraction after transitioning.
• Transgender men on testosterone therapy often report increased libido, and some experience newfound attraction to men.
• Transgender women on estrogen therapy frequently experience a decrease in sexual desire, with some reporting shifts in sexual attraction.
• A 2013 study found that 58.2% of transgender and gender-nonconforming individuals reported changes in sexual attraction over their lifetime, with transgender women more likely to experience these changes after starting HRT.

These findings suggest that while gender identity is deeply ingrained, hormonal changes can influence aspects of sexual orientation.

Functional brain studies also support this concept. A 2008 study found that transgender women who had not started HRT exhibited female-typical hypothalamic responses to certain pheromone-like odors, a response distinct from cisgender men. Similarly, transgender adolescent girls (assigned male at birth) demonstrated brain activity patterns more similar to cisgender girls than cisgender boys, reinforcing the idea that these neurological differences emerge early in life.

Explaining the Science to Those Who May Not Understand

When I began researching this topic, I wasn’t just looking for answers—I was looking for proof that what I felt was real. I wanted to understand why my identity felt so deeply ingrained, despite what society insisted about biology. What I found was both validating and illuminating: the science confirms that being transgender isn’t a choice—it’s an inherent part of who we are.

Many people struggle to understand what it means to be transgender, especially if they are influenced by misinformation or have never met a transgender person. A simple way to explain this is:

“Being transgender isn’t a choice; it’s how a person’s brain is wired. Science shows that the brains of transgender individuals often resemble those of the gender they identify with, not necessarily the sex they were assigned at birth. This difference is biological, and it’s why gender dysphoria happens—it’s like the brain and body are out of sync. Medical transition, including hormone therapy, helps bring the body and brain into alignment, reducing distress and improving well-being. Supporting transgender people isn’t about politics—it’s about recognizing who they truly are and respecting their humanity.”

For those who question the slogan “Trans Women are Women,” the science provides a compelling answer. Gender identity is deeply rooted in brain development, and transgender women have been shown to possess brain structures that align more closely with cisgender women than cisgender men. The term “woman” is not just about chromosomes or reproductive capacity; it is a social and neurological identity shaped by a complex interplay of biology, psychology, and lived experience.

When TERFs or gender-critical individuals ask, “What is a woman?” the most accurate response is, “A woman is someone who identifies and experiences themselves as a woman, and this identity is supported by both social and biological science. Brain studies show that transgender women have neurological patterns that differ from cisgender men and align more closely with cisgender women. To reduce womanhood to mere reproductive function ignores the complexity of human identity and the science behind gender.”

The Bottom Line

As a transgender woman, I’ve often been told that biology is against me, but science tells a different story. Transgender women are not simply “biologically male”—our brains, hormones, and lived experiences paint a much more complex picture. From early brain development through puberty and into adulthood, transgender individuals exhibit biological traits that align with their gender identity, setting them apart from cisgender men.

The brain itself provides some of the strongest evidence, showing structural and functional characteristics that support a transgender woman’s identity long before medical transition. Gender dysphoria isn’t just a feeling—it’s the measurable result of a brain-body incongruence. HRT doesn’t change who we are; it helps align our bodies with the neurological and hormonal reality we’ve always carried.

These findings have real-world implications. They validate the experiences of transgender individuals, offer clarity to families and allies, and demand that policies and laws recognize gender identity beyond outdated binaries. This research underscores the importance of respect, dignity, and equal rights—not as a privilege, but as a fundamental human necessity.

At the end of the day, transgender people aren’t asking for special treatment. We’re asking to be seen for who we truly are. Science supports us. Now, it’s time for society to do the same.

Reference List

• Zhou, J.N., Hofman, M.A., Gooren, L.J., & Swaab, D.F. (1995). A sex difference in the human brain and its relation to transsexuality. Nature, 378(6552), 68–70.
• Kruijver, F.P., Zhou, J.N., Pool, C.W., Hofman, M.A., Gooren, L.J., & Swaab, D.F. (2000). Male-to-female transsexuals have female neuron numbers in a limbic nucleus. The Journal of Clinical Endocrinology and Metabolism, 85(5), 2034–2041.
• Luders, E., Sánchez, F.J., Gaser, C., Toga, A.W., Narr, K.L., & Hamilton, L.S. (2009). Regional gray matter variation in male-to-female transsexualism. NeuroImage, 46(4), 904–907.
• Rametti, G., Carrillo, B., Gómez-Gil, E., Junque, C., Zubiarre-Elorza, L., Segovia, S., & Guillamon, A. (2011). White matter microstructure in female to male transsexuals before cross-sex hormonal treatment. A diffusion tensor imaging study. Journal of Psychiatric Research, 45(2), 199–204.
• Garcia-Falgueras, A., & Swaab, D.F. (2008). A sex difference in the hypothalamic uncinate nucleus: relationship to gender identity. Brain, 131(12), 3132–3146.
• Hulshoff Pol, H.E., Cohen-Kettenis, P.T., Van Haren, N.E., Peper, J.S., Brans, R.G., Cahn, W., & Kahn, R.S. (2006). Changing your sex changes your brain: influences of testosterone and estrogen on adult human brain structure. European Journal of Endocrinology, 155(suppl_1), S107–S114.
• Smith, E.S., Junger, J., Derntl, B., & Habel, U. (2015). The transsexual brain—A review of findings on the neural basis of transsexualism. Neuroscience & Biobehavioral Reviews, 59, 251–266.
• Nguyen, H.B., Chavez, A.M., Lipner, E., Hantsoo, L., Kornfield, S.L., & Epperson, C.N. (2019). What has sex got to do with it? The role of hormones in the transgender brain. Neuropsychopharmacology, 44(1), 22–37.
• Uribe, C., Junque, C., Gómez-Gil, E., Abos, A., Mueller, S.C., & Guillamon, A. (2020). Brain network interactions in transgender individuals with gender incongruence. NeuroImage, 211, 116613.
• Frigerio, A., Ballerini, L., Valdés-Hernández, M., & Caverzasi, E. (2021). Structural, functional, and metabolic brain differences as a function of gender identity or sexual orientation: A systematic review of the human neuroimaging literature. Archives of Sexual Behavior, 50(8), 3329–3350.