The Biology of Gender Identity

By Deirdre Arato, M.Ed, LPC, NCC

As a therapist who has worked with dozens of transgender individuals, I’ve had the privilege of witnessing the courage and authenticity that often defines their journeys. These experiences have underscored the importance of moving beyond simplified or binary views of gender. Today, a growing body of multidisciplinary research supports what many in the transgender community have long expressed: that gender identity, like many aspects of human biology and psychology, exists along a spectrum (Kcomt et al., 2020). By deepening our understanding of the complex interplay between brain, body, and identity, we can foster a more informed, compassionate, and inclusive society—one that respects the dignity and diversity of all people.

Biology and the Brain

Recent research shows that gender identity is influenced by a combination of biological factors, including brain structure, genetics, and early development. For example, a large brain imaging study in 2021 found that the brain structures of transgender people often fall somewhere between those typically seen in cisgender men and women and sometimes resemble the gender they identify with (Altinay et al., 2021). Another study found that even before starting hormone therapy, transgender women had brain characteristics closer to cisgender women (Soleman et al., 2022).

The Role of Genetics and Epigenetics

Genetics also appear to play a role. A 2023 twin study in Australia found that identical twins were more likely to both identify as transgender than fraternal twins, suggesting that gender identity may be partly inherited (Zietsch et al., 2023). Additionally, researchers studying epigenetics—how genes are turned on or off—found many differences in gene expression between transgender and cisgender people, even before any medical transition began (Fernández et al., 2021). These findings support the idea that being transgender is not simply a choice or a social trend—it’s a deeply rooted part of human biology.

Development in the Womb

Multidisciplinary research reveals that a wide range of physical and neurological traits—including sexual orientation and gender identity—develop together during the first half of pregnancy. This early developmental period is shaped by many interacting biological factors such as genetics, epigenetics, the timing and function of sex chromosomes, secretion of sex-determining proteins, gonadal hormone levels, hormone receptor sensitivity, adrenal gland function, maternal diet (including hormones consumed), fetal health, and more (Bao & Swaab, 2011; Hines, 2020; Nugent et al., 2019; O’Hanlan, Gordon, & Sullivan, 2018). For example, studies show that variations in prenatal hormone exposure—especially testosterone and estrogen—can influence brain development in ways that affect gender identity and sexual orientation later in life (Bao & Swaab, 2011). Animal models and human research alike indicate that disruptions or variations in hormone signaling pathways during critical windows of gestation can produce lasting changes in brain structure and behavior linked to gender (Nugent et al., 2019; Arambula & Auger, 2020). Epigenetic mechanisms, which regulate gene activity without changing DNA sequences, are increasingly recognized as key contributors. Epigenetic marks influenced by the intrauterine environment can alter how genes important for sexual development are expressed, further explaining individual differences in gender identity and orientation (Van Dongen et al., 2021). Because these processes occur during a sensitive and formative period, the evidence strongly supports that sexual orientation and gender identity are biological, innate, and largely immutable traits, established before birth. Human development unfolds along a spectrum of possibilities, not a strict male/female binary, reflecting the natural diversity seen in human anatomy and identity (Joel et al., 2015).

Why This Matters

Understanding the biological foundation of gender identity is not just a scientific issue—it’s a human one. When people understand that gender diversity is natural and rooted in biology, acceptance and empathy tend to grow. Science reinforces what therapists, doctors, and many families already know: transgender and gender-diverse people deserve respect, support, and the freedom to live authentically.

References

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Arambula, S. E., & Auger, A. P. (2020). Neuroendocrine mechanisms regulating sex differences in juvenile social play behavior. Frontiers in Behavioral Neuroscience, 14, 40. https://doi.org/10.3389/fnbeh.2020.00040

Bao, A. M., & Swaab, D. F. (2011). Sexual differentiation of the human brain: Relation to gender identity, sexual orientation and neuropsychiatric disorders. Frontiers in Neuroendocrinology, 32(2), 214–226. https://doi.org/10.1016/j.yfrne.2010.03.003

Fernández, R., Guillamon, A., Gómez-Gil, E., & Esteva, I. (2021). Epigenetics of transgender identity. Scientific Reports, 11, 20371. https://doi.org/10.1038/s41598-021-99896-5

Hines, M. (2020). Gender development and the human brain. Annual Review of Neuroscience, 43, 69–88. https://doi.org/10.1146/annurev-neuro-090919-022429 Joel, D., Berman, Z., Tavor, I., Wexler, N., Gaber, O., Stein, Y., ... & Assaf, Y. (2015). Sex

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Soleman, R. S., Wang, Y., Tang, S., Frick, A., & Spitzer, S. (2022). Brain sex differentiation in transgender individuals prior to hormone therapy. Cerebral Cortex, bhac090. https://doi.org/10.1093/cercor/bhac090

Van Dongen, J., Lindquist, M., & Shinn, A. (2021). Epigenetics and the prenatal environment: A review of the evidence and implications for gender identity. Journal of Developmental Origins of Health and Disease, 12(3), 333–345. https://doi.org/10.1017/S2040174420001073

Zietsch, B. P., Vassos, E., McGrath, J. J., & Kirk, K. M. (2023). Capturing gender diversity in twin research. Twin Research and Human Genetics, 26(1), 40–49. https://doi.org/10.1017/thg.2022.34