Every human embryo starts with the same undifferentiated tissue between its legs, and the path that tissue takes depends on a chain of hormonal signals that can play out differently from what the chromosomes would predict. A girl can have a penis because the biological ingredients that shape genital anatomy, the genes that guide gender identity, and the chromosomes that define genetic sex are three separate systems that usually align but sometimes don’t. This happens through well-documented intersex conditions and, separately, through the experience of transgender identity, where a person’s internal sense of their gender diverges from the body they were born with.
Everyone Starts with the Same Equipment
For roughly the first six weeks after conception, embryos with XX chromosomes and embryos with XY chromosomes look identical in the structures that will eventually become genitals. The tissue that can become either a clitoris or a penis is called the genital tubercle, and it sits there waiting for instructions. Those instructions come primarily from hormones, not directly from chromosomes. The gene SRY on the Y chromosome triggers the development of testes, but it is the hormones those testes produce that do the actual work of shaping the external anatomy.
In a typical XY embryo, the testes begin producing testosterone, and an enzyme in the genital tubercle converts that testosterone into a more potent hormone called dihydrotestosterone, or DHT. DHT is the key signal that drives the genital tubercle to develop into a penis and scrotum. In studies of fetal development, DHT levels in the genital tubercle of males rise steadily during the critical window of sexual differentiation, while in females they remain far lower.1Journal of Steroid Biochemistry. Testosterone and dihydrotestosterone in sexual ducts and genital tubercle of rabbit fetuses during sexual organogenesis: Effects of fetal decapitation The enzyme that makes this conversion, 5-alpha reductase, is expressed in the tissue surrounding the genital tubercle, and without it, even a genetically male embryo’s external genitals won’t fully masculinize.2Biology of Reproduction. Prenatal low-dose methyltestosterone, but not dihydrotestosterone, treatment induces penile formation in female mice and guinea pigs
What this means is that the presence or absence of a penis is ultimately a hormone story, not a chromosome story. Chromosomes set up the usual hormonal cascade, but if that cascade is interrupted or redirected, the anatomy that results can be very different from what the chromosomes would suggest.
Intersex Conditions Where Anatomy and Chromosomes Diverge
There are several well-characterized medical conditions in which a person’s external genitals don’t match their chromosomal sex. These are the clearest biological pathways through which a girl can have a penis, or a person with XY chromosomes can have entirely female-appearing anatomy.
Congenital Adrenal Hyperplasia
Congenital adrenal hyperplasia, or CAH, is the most common cause of ambiguous genitalia in chromosomally female (46,XX) newborns. In CAH, an enzyme deficiency in the adrenal glands causes the body to overproduce androgens, the family of hormones that includes testosterone. When this happens during fetal development, the excess androgens masculinize the external genitals of a genetically female fetus.3PubMed Central. Classic congenital adrenal hyperplasia: A delayed presentation The result can range from a mildly enlarged clitoris to fully formed male-appearing genitalia, even though the child has ovaries and a uterus internally.
In severe cases, the virilization can be so complete that the child is initially identified as male at birth. Published case reports describe 46,XX children with CAH who were raised as boys before the diagnosis was made, sometimes not until years later.4PubMed Central. To Which Gender Should External Genitalia be Corrected in a Lately Diagnosed 46,XX Congenital Adrenal Hyperplasia Case with Severe Virilization: Case Report Clinical guidelines have traditionally recommended female sex assignment for these children when ovaries and internal female organs are present, regardless of how masculinized the external anatomy appears.5PubMed. Approach to assigning gender in 46,XX congenital adrenal hyperplasia with male external genitalia: replacing dogmatism with pragmatism But as the title of that guideline hints, there has been a shift toward more individualized approaches.
Complete Androgen Insensitivity Syndrome
If CAH shows how a genetically female body can develop male anatomy, complete androgen insensitivity syndrome (CAIS) illustrates the reverse. A person with CAIS has XY chromosomes and internal testes that produce testosterone, but their body’s cells cannot respond to androgens at all. Because the genital tubercle never receives the masculinizing signal, the external genitals develop along female lines. People with CAIS are born looking entirely female, are typically raised as girls, and in many cases don’t learn about their chromosomal makeup until puberty fails to produce menstruation, or until medical imaging for another reason reveals the absence of a uterus and the presence of internal testes.6PubMed Central. Complete androgen insensitivity syndrome in three sisters
CAIS is a striking example of how chromosomes alone don’t determine what a person looks like or, in most cases, who they feel themselves to be. The vast majority of people with CAIS identify as women and live as women throughout their lives.
5-Alpha Reductase Deficiency
A third condition, 5-alpha reductase deficiency, produces perhaps the most dramatic developmental timeline. Children with this condition have XY chromosomes and testes, but lack the enzyme that converts testosterone to DHT in the genital tubercle. Because DHT is what drives external masculinization in the womb, these children are born with female-appearing or ambiguous genitals and are often raised as girls. Then, at puberty, the surge of testosterone causes the genitals to masculinize: the clitoris-like structure grows into a penis, the testes descend, and the body takes on a more typically male appearance. This condition has been documented in clusters within certain populations.7PubMed. Gender identity and role in a pedigree of Arabs with intersex due to 5 alpha reductase-2 deficiency
What happens to gender identity in these cases varies. Some individuals who were raised as girls transition to living as men after the pubertal changes, while others continue identifying as women. The diversity of outcomes underscores that gender identity isn’t automatically dictated by either chromosomes or genital anatomy.
Chromosomal Mosaicism
Beyond single-gene conditions, some people are born with unusual combinations of sex chromosomes in different cells of their body. Rather than being uniformly XX or XY, they carry mixtures such as some cells with one X, some with XY, and others with different combinations. These mosaic patterns can produce ambiguous genitalia and a range of reproductive anatomies that don’t fit neatly into male or female categories.8Annals of Clinical and Laboratory Science. A Novel Sex Chromosome Mosaicism 45,X/45,Y/46,XY/46,YY/47,XYY Causing Ambiguous Genitalia These cases remind us that even chromosomal sex itself isn’t always a clean binary.
How Common Are Intersex Variations
The prevalence of intersex conditions depends heavily on how you define the term, and this has been a genuine source of scientific debate. A widely cited figure of about 1.7 percent of the population comes from a broad definition that includes any deviation from the “Platonic ideal” of male or female, encompassing conditions like late-onset CAH that may never produce visible genital differences. A narrower definition, limited to conditions where chromosomal sex is inconsistent with genital anatomy or where the genitals are genuinely ambiguous, produces a figure closer to about 0.018 percent.9PubMed. How common is intersex? a response to Anne Fausto-Sterling That’s roughly 1 in 5,500 births. The gap between these estimates is about a hundredfold, and which number you encounter depends on the context in which it’s being used.
Neither number is “wrong” in an absolute sense; they’re answering different questions. The broader figure captures every variation in the system of sex development, while the narrower one captures the cases where something visibly atypical is present at birth. For the specific question of how often a child is born with genitals that don’t match their chromosomes in an obvious way, the smaller number is more relevant.
Gender Identity Is Built Separately from Anatomy
Intersex conditions explain how a body can develop genitals that don’t match its chromosomes. But the question in the article’s title also touches on gender identity, which is a person’s internal sense of being a girl, a boy, both, or neither. This is where the conversation expands beyond intersex conditions to include transgender experience.
Research strongly suggests that gender identity is shaped in significant part by the prenatal hormone environment, particularly testosterone exposure during key windows of brain development. Evidence from animal studies, measurements of hormone-linked physical traits, and studies of people with intersex conditions all point toward the same conclusion: the brain’s sense of gender is organized early in development and influenced by the same hormones that shape the genitals, but at a different time and through different mechanisms.10PubMed Central. Neurobiology of gender identity and sexual orientation Prenatal testosterone exposure is linked to more male-typical play behavior, spatial abilities, and in some cases gender identity, across a range of study designs.11PubMed. Gender development and the human brain
The important takeaway is that the brain’s development and the genitals’ development are separate processes that usually happen in coordination but can diverge. A fetus could be exposed to one hormonal environment during the window when genitals are forming and a somewhat different one during the window when the brain regions involved in gender identity are being organized. This is one plausible explanation for transgender identity: the body developed one way, but the brain’s gender-relevant wiring developed another.
What Brain Research Shows
Neuroimaging studies of transgender individuals have found patterns that support the idea of a biological basis for gender identity. Research using brain scans to measure cortical thickness and the structure of white-matter tracts has found that transgender women (assigned male at birth, identifying as female) show a mix of regions that look typically female, typically male, and distinct from both. Transgender men show a similar but reversed mixture. In other words, the brains of transgender individuals aren’t simply “male brains in female bodies” or vice versa; they have their own characteristic patterns that sit between and outside the typical male and female ranges.12PubMed Central. A Review of the Status of Brain Structure Research in Transsexualism
This research is still evolving and has real limitations. Sample sizes are often small, and it’s difficult to disentangle the effects of hormone therapy (which many transgender adults have undergone) from innate brain differences. But the consistent finding that transgender brains show patterns distinct from those of cisgender people of either sex adds weight to the idea that gender identity has a neurobiological component that isn’t reducible to social learning alone.
The Genetics Question Remains Open
If the prenatal hormone environment shapes gender identity, a natural follow-up is whether genetics plays a role in who develops a gender identity that doesn’t match their body. Twin studies have hinted at a heritable component, but the search for specific genes has been frustrating. One exome sequencing study of transgender individuals identified 21 genetic variants across 19 genes involved in sexually dimorphic brain development, but these were candidate findings rather than confirmed causes.13Scientific Reports. The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants Other studies looking at genes related to sex hormone receptors and enzymes found no significant differences between transgender and cisgender individuals.14PubMed. Association study of gender identity disorder and sex hormone-related genes
The current scientific consensus is that genetics probably contributes, but no single gene or even a reliable set of genes has been identified.15PubMed Central. Brain Sex Differences Related to Gender Identity Development: Genes or Hormones? Gender identity is most likely influenced by many genes acting in concert with the prenatal hormonal environment, social factors, and individual developmental experiences. This is the kind of complex trait where looking for a single explanatory gene was always unlikely to succeed.
How Gender Identity Develops in People Born with Intersex Traits
One of the most informative windows into how gender identity works comes from long-term follow-up studies of people who were born with intersex conditions and assigned a sex at birth. For decades, the prevailing medical view was that a child’s gender identity would follow their sex of rearing as long as the assignment was made early and the family was committed to it. The evidence supports this to some extent, but with important exceptions.
A multicenter study of 30 individuals with various intersex conditions in India found that about 90 percent retained the gender they were assigned and raised in. But roughly 10 percent experienced discordance, including cases where individuals who had undergone genital surgery as children later transitioned to a different gender.16PubMed Central. Long-term Outcomes of Gender Decisions in Differences of Sex Development (DSD) from an Indian Perspective: A Multicenter Study In a European study evaluating individuals with conditions including CAH, CAIS, partial androgen insensitivity, and 5-alpha reductase deficiency, most participants with XY chromosomes who had been assigned female at birth continued to live as women. Exceptions occurred most often in people with partial androgen insensitivity, where the hormonal picture during development is more mixed.17The Journal of Sexual Medicine. Gender Assignment and Medical History of Individuals with Different Forms of Intersexuality: Evaluation of Medical Records and the Patients’ Perspective
These findings suggest that the sex you’re raised as has a real influence on gender identity, but it isn’t the whole story. In a meaningful minority of cases, biology reasserts itself despite years of socialization in a particular gender role. The children who later transition aren’t confused or making a whimsical choice; they’re responding to an internal sense of identity that socialization couldn’t override.
The Ethics of Early Genital Surgery
When a baby is born with ambiguous genitalia, families and medical teams face a decision with lifelong consequences: what sex to assign, and whether to perform surgery to make the genitals look more typical. For decades, the standard approach was to operate in infancy, usually to feminize the genitals, on the theory that it was easier to construct female-appearing anatomy and that the child’s identity would follow.
That approach has come under serious ethical scrutiny. The core argument against early surgery is straightforward: the operation is irreversible, the child cannot consent, and in a meaningful percentage of cases the surgical outcome won’t match the person’s eventual gender identity. Ethical analysis increasingly supports the position that surgery for intersex infants should be delayed until the individual can participate in the decision, unless there’s a genuine medical need such as urinary obstruction.18PubMed Central. A principled ethical approach to intersex paediatric surgeries
This shift represents a significant change in medical culture. Surgeons who trained in the older paradigm were taught to “fix” ambiguous genitalia as quickly as possible, partly to reduce parental distress and partly based on now-questioned assumptions about how gender identity works. The move toward deferral acknowledges that the person whose body is being altered has more at stake than anyone else in the room and deserves a voice in the decision.
Why the Language Keeps Changing
If you’ve encountered the terms “intersex,” “disorders of sex development” (DSD), and “differences of sex development” all used for the same conditions, you’re not alone in finding it confusing. The medical community adopted “disorders of sex development” in a 2006 consensus statement, partly to create a shared clinical vocabulary. Many intersex advocates pushed back against the word “disorder,” arguing it pathologizes natural human variation. “Differences of sex development” emerged as a compromise that keeps the DSD abbreviation but drops the implication that something is broken.
Among people who live with these conditions, preferences vary widely. Some prefer “intersex” as a straightforward identity term. Others prefer DSD language because it grounds their experience in specific, diagnosable medical conditions rather than an identity label they may not want. Still others use both depending on context. There is no single correct term, and the choice often says more about the speaker’s values and community than about biology itself. What matters for understanding the science is recognizing that all these terms describe real, documented variations in how sex develops, not theoretical abstractions or lifestyle choices.
How Intersex and Transgender Experiences Overlap and Differ
The title question bundles two related but distinct phenomena. Intersex conditions involve a measurable biological variation in chromosomes, hormones, or anatomy. Transgender identity involves a mismatch between a person’s felt sense of gender and the sex they were assigned at birth, usually in the absence of any detectable intersex condition. These are different starting points that sometimes lead to similar lived experiences.
A person with CAIS has XY chromosomes, identifies as female, and lives as a woman. A transgender woman has XY chromosomes, identifies as female, and lives as a woman. From the outside, the end result can look identical, but the biological pathway differs. In the CAIS case, the body developed female anatomy autonomously. In the transgender case, the body developed male anatomy, and the person may seek medical intervention to align their body with their identity.
What both experiences share is that they challenge the assumption that chromosomes, hormones, genitals, and gender identity always travel together as a package. In most people they do. But the existence of intersex conditions proves the biological mechanisms can diverge, and the existence of transgender identity suggests that the brain’s gender wiring can diverge from the body’s physical development even when no chromosomal or hormonal anomaly is detectable with current tools. The science of why this happens is still being assembled, but the reality that it happens is not in scientific dispute.