Biological sex in humans develops through a cascade of genetic signals, hormonal triggers, and cellular responses that unfolds over weeks of embryonic life, and variation can arise at virtually any step. The conditions historically grouped under the term “intersex,” now more commonly called differences of sex development (DSD), stem from dozens of distinct genetic and hormonal pathways. Far from a simple binary switch, sex development depends on the coordinated action of genes on both sex chromosomes and autosomes, the hormones those genes help produce, and even the regulatory elements that control when and where those genes turn on.
The Genetic Cascade That Launches Male Development
The gene most people associate with male sex determination is SRY, located on the Y chromosome. Discovered in 1990, SRY encodes a protein that binds DNA and sets off a chain of events directing an undifferentiated embryonic gonad toward becoming a testis.1PubMed. Sry and SoxE genes: How they participate in mammalian sex determination and gonadal development? But SRY doesn’t do the heavy lifting alone. Its main job is to activate another gene called SOX9, which in turn drives the formation of Sertoli cells, Leydig cells, blood vessel structures, and the testis cords that give the organ its shape.2Molecular Endocrinology. SRY and the Standoff in Sex Determination
The link between SRY and SOX9 turns out to hinge on specific enhancer sequences upstream of the SOX9 gene. Research has shown that duplicating or deleting these enhancers can cause complete sex reversal: individuals with two X chromosomes and no Y can develop testes if the enhancers are duplicated, while individuals with a Y chromosome can develop as female if those same enhancers are deleted.3Nature Communications. Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9 One particular enhancer, called Enh13, sits within a region whose deletion in humans is associated with XY sex reversal, suggesting it plays a critical role in our species as well.4PubMed Central. Sex reversal following deletion of a single distal enhancer of Sox9 These findings reveal that even when SRY is present and intact, the downstream wiring has to be correctly connected or the signal never reaches its target.
Ovarian Development Is Not a Default
For decades, textbooks described female development as what happens “by default” in the absence of SRY. That framing has been overturned. Ovarian development requires its own set of actively expressed genes. WNT4, for instance, suppresses male-typical pathways, promotes the formation of Müllerian duct structures (which become the uterus and fallopian tubes), and helps maintain oocyte health. Its expression appears to be regulated by another protein called RSPO1.5PubMed. WNT4, RSPO1, and FOXL2 in sex development Mutations in these genes can lead to virilization or gonadal abnormalities in XX individuals, underscoring that female development is an active, genetically directed process, not merely the absence of maleness.
This reframing matters because it means there are two competing genetic programs running in parallel during early embryonic life. The outcome depends on which program gains the upper hand. If the male program stalls, even partially, elements of the female program can assert themselves, and vice versa. That tug-of-war helps explain why DSD conditions exist on a spectrum rather than falling neatly into a handful of categories.
When Hormone Pathways Diverge
Even after the gonads form, the story is far from over. Hormones produced by those gonads, and the body’s ability to respond to them, shape external and internal anatomy in ways that can diverge from chromosomal sex. Three of the most well-characterized hormone-related DSD conditions illustrate this.
Androgen Insensitivity Syndrome
Androgen insensitivity syndrome (AIS) is caused by mutations in the androgen receptor gene on the X chromosome. In the complete form, a person with XY chromosomes and functioning testes produces testosterone normally, but their cells cannot respond to it. The result is external genitalia that appear entirely female, despite the presence of internal testes. Partial forms produce a range of appearances, from mostly female to mostly male with features such as hypospadias or micropenis.6PubMed. Androgen insensitivity syndrome: clinical features and molecular defects Many individuals with complete AIS are not diagnosed until puberty, when menstruation doesn’t begin, or even later. Because the testes produce enough estrogen (through peripheral conversion of testosterone) to trigger breast development, these individuals often go through a largely typical-appearing female puberty.
5-Alpha Reductase Deficiency
A fully virilized male phenotype requires not just testosterone but also dihydrotestosterone (DHT), which is produced from testosterone by the enzyme 5-alpha reductase type 2. When the gene for this enzyme (SRD5A2) carries mutations on both copies, affected XY individuals may be born with ambiguous or female-appearing genitalia but then virilize dramatically at puberty when rising testosterone levels partially compensate.7PubMed Central. Mutations in AR or SRD5A2 Genes: Clinical Findings, Endocrine Pitfalls, and Genetic Features of Children with 46,XY DSD This condition gained public attention through reports from communities in the Dominican Republic and Papua New Guinea where it occurs at unusually high frequencies due to founder effects. The local term “güevedoces,” roughly translating to “male genitals at twelve,” captures the dramatic pubertal shift.
Congenital Adrenal Hyperplasia
Congenital adrenal hyperplasia (CAH) is the most common DSD affecting XX individuals. The vast majority of cases involve a deficiency of the enzyme 21-hydroxylase, caused by mutations in the CYP21A2 gene on chromosome 6.8PubMed. Steroid 21-hydroxylase deficiency in congenital adrenal hyperplasia When this enzyme doesn’t work properly, the adrenal glands can’t make enough cortisol and aldosterone, and steroid precursors get shunted into androgen production instead.9PubMed Central. The clinical and biochemical spectrum of congenital adrenal hyperplasia secondary to 21-hydroxylase deficiency In genetic females, the excess androgens during fetal development can virilize the external genitalia, sometimes substantially. The classic form of 21-hydroxylase deficiency occurs in roughly 1 in 16,000 births, and the most severe cases involve salt-wasting that requires immediate medical attention in the newborn period.10The Journal of Clinical Endocrinology & Metabolism. Genetics and Pathophysiology of Classic Congenital Adrenal Hyperplasia Due to 21-Hydroxylase Deficiency
Chromosomal Variation and Chimerism
Some DSD conditions arise not from single-gene mutations but from having an atypical set of sex chromosomes altogether. Klinefelter syndrome (47,XXY) results when sex chromosomes fail to separate properly during the formation of egg or sperm cells, producing an individual with two X chromosomes and one Y.11PubMed Central. Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage People with Klinefelter syndrome are typically raised male and have testes, but the extra X chromosome can affect testicular function, testosterone production, and fertility.
Rarer still is chimerism, in which a single individual carries cell lines from two genetically distinct embryos that fused early in development. If one embryo was XX and the other XY, the resulting person has both XX and XY cells distributed throughout their body.12OBM Genetics. 46,XX/46,XY Chimerism & Human Sexual Development This is distinct from mosaicism, which arises from errors after a single embryo has already begun dividing. Depending on how the cell lines distribute, chimeric individuals can develop ovarian tissue in one gonad and testicular tissue in the other, a condition now called ovotesticular DSD. Ovotesticular DSD is the rarest form of DSD in humans and characteristically presents with ambiguous genitalia.13PubMed Central. Ovotesticular Disorder of Sex Development: An Unusual Presentation
Persistent Müllerian Duct Syndrome
During typical male development, the testes produce anti-Müllerian hormone (AMH), which causes the Müllerian ducts to regress. Without that signal, the ducts persist and develop into a uterus and fallopian tubes. Persistent Müllerian duct syndrome (PMDS) is an autosomal recessive condition in which XY individuals who appear outwardly male retain these internal female reproductive structures.14PubMed. Two heterozygous mutations of the AMH gene in a Japanese patient with persistent Müllerian duct syndrome Over 50 different mutations in the AMH gene have been identified, along with mutations in its receptor gene, AMHR2.15PubMed. Molecular genetics of the persistent müllerian duct syndrome: a study of 19 families PMDS is often discovered incidentally during surgery for undescended testes, surprising both families and clinicians. It underscores how internal and external anatomy can follow different developmental scripts within the same individual.
How Common Are These Conditions
The question of prevalence is surprisingly contentious and depends almost entirely on where you draw the line. A frequently cited figure of 1.7% comes from work by biologist Anne Fausto-Sterling, but that number includes conditions like Klinefelter syndrome, Turner syndrome, and late-onset adrenal hyperplasia, which many clinicians do not classify as intersex because the individuals involved usually have unambiguous anatomy and develop along typical lines. Under a stricter definition, limited to cases where chromosomal sex is inconsistent with phenotypic sex or where the phenotype cannot be classified as clearly male or female, the prevalence drops to about 0.018%, roughly 100 times lower.16PubMed. How common is intersex? a response to Anne Fausto-Sterling
Neither number is wrong in an absolute sense; they answer different questions. The broader figure captures anyone whose sex chromosomes, gonads, or hormonal profile departs from the most common patterns. The narrower figure captures conditions where the departure creates clinical ambiguity. Which figure matters depends on the context: advocacy discussions often favor the broader count, while clinical genetics tends to use the narrower one. What both agree on is that biological variation in sex development is not vanishingly rare, even under the strictest definitions.
Terminology and the Shift Toward “Differences of Sex Development”
The language used to describe these conditions has changed substantially. Older terms like “hermaphrodite,” “pseudohermaphrodite,” and even “intersex” were considered confusing and potentially stigmatizing. In 2005, a consensus conference in Chicago recommended adopting the umbrella term “disorders of sex development” (DSD), defined by the underlying genetic, hormonal, or anatomical features rather than by loaded historical labels.17PubMed Central. Disorders of sex development Some affected individuals and advocacy groups prefer “differences” over “disorders” to avoid implying pathology where none may be felt. Others retain “intersex” as a community identity term. In clinical and research literature, DSD has become the standard, but the terminology debate remains active and personal.
Epigenetic Regulation Adds Another Layer
Beyond the DNA sequence itself, the timing and location of gene expression during sex development are controlled by epigenetic mechanisms, chemical modifications to DNA and the proteins around it that determine whether a gene is accessible or silenced. The SRY gene, for example, must be activated in a precise window during embryonic life, and that activation depends not only on specific transcription factors but on the epigenetic machinery ensuring the right chromatin state at the right moment.18PubMed. Epigenetic regulation of mammalian sex determination If the epigenetic timing slips, even an intact SRY gene may fail to trigger the male developmental cascade, potentially contributing to DSD in individuals whose DNA sequence looks normal under standard genetic testing.
This helps explain a frustrating clinical reality: a substantial fraction of DSD cases currently have no identified genetic cause. Standard sequencing finds no mutations in any known gene. The answer may lie in regulatory elements, enhancer sequences, or epigenetic patterns that current diagnostic methods don’t routinely capture.
Gender Identity, Hormones, and the Brain
One of the most sensitive questions surrounding DSD is how sex development affects gender identity. Historically, the assumption was that gender identity could be shaped primarily by socialization, leading some clinicians to assign a sex at birth and surgically alter ambiguous anatomy to match. Outcomes from that era were mixed and sometimes disastrous, particularly in cases where the assigned sex conflicted with the individual’s eventual sense of self.
Research now suggests that prenatal hormones play a role in shaping brain structures associated with gender identity, though the relationship is far from deterministic.19PubMed Central. Brain Sex Differences Related to Gender Identity Development: Genes or Hormones? Genetic components also appear to contribute, though no single gene has been identified as a driver.20Journal of Urology. Androgen Imprinting of the Brain in Animal Models and Humans With Intersex Disorders: Review and Recommendations The current clinical consensus recognizes that biological factors including genetics and hormones interact with psychological, social, and cultural influences in complex ways.21PubMed. Deciding on gender in children with intersex conditions: considerations and controversies The practical upshot is a move away from early irreversible surgical interventions and toward approaches that preserve options until the individual can participate in decisions about their own body.
How Genetic Testing Has Changed Diagnosis
For a long time, diagnosing the specific cause of a DSD condition was a painstaking process. Clinicians would test one gene at a time based on clinical suspicion, and many patients went undiagnosed. Next-generation sequencing (NGS) panels that screen dozens of DSD-related genes simultaneously have changed this landscape. One clinical study using an NGS panel confirmed a molecular diagnosis in about a third of patients tested, identifying mutations in genes including AMH, AR, SRD5A2, and others, and in several cases the diagnosis directly changed how those patients were managed.22PubMed Central. Next generation sequencing (NGS) to improve the diagnosis and management of patients with disorders of sex development (DSD) Another study found that NGS achieved a diagnostic yield of about 28%, nearly three times the rate of the single-gene tests clinicians had been ordering previously.23Scientific Reports. Diagnostic Application of Targeted Next-Generation Sequencing of 80 Genes Associated with Disorders of Sexual Development
Still, that means the majority of DSD patients tested by NGS do not receive a definitive genetic answer. The unresolved cases likely include conditions caused by variants in genes not yet recognized as DSD-related, by structural changes in regulatory DNA, or by epigenetic alterations that sequencing alone cannot detect. Whole-genome sequencing and functional studies are gradually filling these gaps, but a complete genetic accounting of DSD remains a work in progress.
Fertility Preservation and Reproductive Options
Fertility is a concern for many people with DSD, and historically it received little clinical attention because of a focus on sex assignment and genital surgery. That is changing. Advances in assisted reproductive technology and tissue cryopreservation now offer options that did not exist a generation ago.24PubMed. Fertility in differences of sex development patients Testicular and ovarian tissue cryopreservation, already offered to children facing cancer treatment, is being extended to individuals with DSD whose gonads may be removed for medical reasons or whose gonadal function may decline over time.25PubMed Central. Preservation of Fertility Potential for Gender and Sex Diverse Individuals
Evidence suggesting that some individuals with DSD retain reproductive potential in their gonadal tissue has encouraged researchers to advocate for the same fertility counseling and preservation access that other patient groups receive.26PubMed. Establishing reproductive potential and advances in fertility preservation techniques for XY individuals with differences in sex development The data are still limited and the science is still maturing, but the direction is clear: reproductive possibilities should be discussed early and honestly, rather than treated as an afterthought.
Sex Reversal in Other Species
Humans are not the only vertebrates in which the genetic sex and the physical sex can diverge. In many fish, amphibians, and reptiles, environmental factors like temperature during development can override the genetic sex-determination system entirely. Individuals with one genetic sex develop the gonads and reproductive function of the other, a phenomenon formally called sex reversal.27PubMed Central. Climate-driven shifts in adult sex ratios via sex reversals: the type of sex determination matters These reversals are not anomalies in these species; they occur regularly and can shift population sex ratios in response to climate changes. Mammalian sex determination is considerably more buffered against environmental influence, relying heavily on genetic signals like SRY and SOX9. But the existence of environmental sex reversal across vertebrates is a reminder that sex-determination systems are evolved, variable, and less rigidly binary across the tree of life than popular imagination tends to assume.