Gender dysphoria doesn’t have a single, definitive cause. The best available evidence points to a combination of biological factors, primarily involving genetics, prenatal hormone exposure, and brain development, that together shape a person’s gender identity. No one factor explains every case, and scientists are still working to understand how these influences interact.
About 1% of people aged 13 and older in the United States, roughly 2.8 million people, identify as transgender. The rates are notably higher among younger age groups: 3.3% of teens aged 13 to 17 and 2.7% of young adults aged 18 to 24, compared to 0.4% of adults aged 35 to 64.
Gender Dysphoria vs. Gender Incongruence
Before getting into causes, it helps to understand what gender dysphoria actually refers to clinically. The DSM-5 defines it as a marked incongruence between a person’s experienced gender and their assigned sex, lasting at least six months, that causes significant distress or impairment in daily life. The distress is the key part. Being transgender isn’t itself a disorder; gender dysphoria specifically describes the distress that can accompany that experience.
The World Health Organization made this distinction more explicit in 2022 when the ICD-11 replaced older terms like “transsexualism” and “gender identity disorder” with “gender incongruence,” and moved the diagnosis out of the mental health chapter entirely. It now sits under “conditions related to sexual health,” reflecting the scientific position that gender diversity is not a form of mental illness.
Prenatal Hormones and Brain Development
The strongest line of evidence for a biological cause involves hormones in the womb. During fetal development, the brain and the genitals develop on different timelines. External genitalia form around 6 to 8 weeks of gestation, while the brain regions involved in gender identity develop later, in the second half of pregnancy. This gap creates a window where the two processes could be influenced differently.
Testosterone plays a central role. In typical male development, testosterone acts on brain regions containing hormone receptors and produces lasting organizational changes in areas related to sexual behavior and identity. Female development, by contrast, proceeds in the absence of significant testosterone exposure. Importantly, the brain and genitals respond to different forms of testosterone. The genitals are shaped by dihydrotestosterone, while the brain appears to respond primarily to testosterone itself. This means conditions that alter one hormone but not the other can produce a mismatch between physical anatomy and brain-based gender identity.
This isn’t just theoretical. Studies of people born with certain differences in sex development show an exposure-dependent pattern: the more prenatal androgen exposure, the more likely a person is to develop a male gender identity, regardless of how their external anatomy looks at birth. Only some people exposed to atypical prenatal hormone environments develop a different gender identity than expected, though, which means hormones are a predisposing influence rather than a guarantee.
Genetic Influences
Twin studies provide the clearest window into whether genes play a role, and they suggest genetics matter, though estimates of how much vary widely. Studies have placed the heritability of gender variance anywhere from 11% to 70%. One widely cited estimate puts it at 62%, while another found heritability of 41% among adolescents assigned female at birth but only 11% among adults assigned female, and no measurable genetic effect for those assigned male.
A large population-based twin study from Sweden found something striking: no same-sex twin pairs where both twins had a gender dysphoria diagnosis were identified, while 37% of different-sex twin pairs were concordant. This unexpected finding complicates the picture and suggests that shared genetics alone don’t explain concordance patterns.
Researchers have also identified specific gene variants that may contribute. One study found that transgender women tend to have longer repeat sequences in the androgen receptor gene compared to cisgender men. A longer repeat sequence makes the receptor less efficient at picking up testosterone signals, which could reduce the masculinizing effect of hormones on the brain during development. A separate association was found between the CYP17 gene, which encodes an enzyme involved in hormone production, and transgender men. These are statistical associations in relatively small studies, not definitive causes, but they point toward the hormone-signaling pathway as a likely area of genetic influence.
Brain Structure Differences
Neuroimaging research has found that the brains of people with gender dysphoria often show structural patterns that don’t fully match either their assigned sex or their experienced gender, but tend to shift toward the latter. Transgender women, for example, have been found to have smaller gray matter volume in the left somatosensory and motor cortices, a pattern more similar to cisgender women than cisgender men. Studies of transgender teenagers found that hypothalamic responses, the brain’s hormonal control center, more closely resembled those of the gender the person identified with rather than the sex they were assigned at birth.
Research on people who have undergone gender-affirming surgery has found that cognitive, emotional, and sensorimotor brain regions align with their experienced gender. These findings are consistent with the idea that gender identity has a neurological basis, though it remains unclear whether these brain differences are a cause of gender dysphoria, a consequence of living with a particular gender identity, or both.
Why There’s No Single Explanation
The diversity of gender expression across human populations argues strongly against any simple or unitary cause. Biological factors like genetics and prenatal hormones clearly contribute, but none of the mechanisms identified so far can account for all of the variation in gender identity. Many people exposed to atypical prenatal hormone environments develop a gender identity consistent with their assigned sex. Many transgender people have no identifiable hormonal or genetic difference at all.
What the research does make clear is that gender identity has a significant biological component. It is not simply a choice or the product of upbringing. The interplay between genes, hormone levels, hormone receptor sensitivity, and brain development during critical windows before birth creates the conditions under which gender identity forms. How social and psychological factors may interact with that biological foundation remains one of the open questions, but the biological contribution itself is well established.