Boy and girl twins are almost always fraternal, not identical. Identical twins form from a single fertilized egg that splits in two, so both embryos carry the same set of chromosomes, including the same sex chromosomes. A pair with one boy and one girl nearly always started as two separate eggs fertilized by two separate sperm. The rare exceptions involve chromosomal accidents or an unusual fertilization event so uncommon it has been documented only a handful of times in the medical literature.
How Identical Twins Form and Why Sex Normally Matches
Identical, or monozygotic, twins arise when a single fertilized egg splits during the earliest stages of development, before the embryo implants in the uterus.{1Nature Communications. Identical twins carry a persistent epigenetic signature of early genome programming} Because both halves come from the same original cell, they inherit the same nuclear DNA. That includes the pair of sex chromosomes: either two X chromosomes (female) or one X and one Y (male). If the original egg was fertilized by a Y-carrying sperm, both twins get that Y. If it was fertilized by an X-carrying sperm, neither twin has a Y. Under normal circumstances, there is no mechanism for the split to sort one sex chromosome into one twin and a different one into the other.
Fraternal, or dizygotic, twins are a different story. Two eggs are released and fertilized independently, each by its own sperm cell. Each fertilization is a fresh coin toss for sex. Roughly half of all fraternal twin pairs end up as one boy and one girl. So when a parent expecting twins learns there is one of each, the assumption in the clinic is that the pregnancy is fraternal. That assumption is correct the vast majority of the time, but not every time.
When Chromosomes Go Missing After the Split
The best-documented route to identical twins of apparently different sex involves an error in chromosome handling shortly after the egg splits. The original fertilized egg is 46,XY, meaning it is genetically male. During one of the very first cell divisions, one daughter cell loses its Y chromosome. If the embryo then splits into twins, one twin can end up with a normal 46,XY set of chromosomes while the other ends up with a 45,X set, a condition known as Turner syndrome. The twin missing the Y develops along a female pathway, though typically with the health features that come with Turner syndrome, including short stature and usually infertile ovaries.
This has been diagnosed prenatally. In one reported case, ultrasound revealed a monochorionic twin pregnancy where the fetuses appeared to be different sexes. Amniocentesis of both sacs confirmed mosaicism involving a Y-chromosome rearrangement, with different proportions of the mosaic cell lines in each twin.{2PubMed. Prenatal diagnosis of heterokaryotypic mosaic twins discordant for fetal sex} In two other prenatal cases, monochorionic twins were found where one fetus had a 45,X karyotype and the other had 46,XX, both confirmed as monozygotic by genetic testing.{3Fetal Diagnosis and Therapy. Prenatal Diagnosis and Management of Monozygotic Twins Discordant for Turner Syndrome}
The term for this situation is heterokaryotypic monozygotic twinning. It is extremely rare, and diagnosing it requires amniocentesis of both sacs individually, because sampling only one sac or testing placental tissue can miss the discrepancy entirely.{4Journal of Fetal Medicine. Heterokaryotypic Monochorionic Twin Pregnancy: New Perspective} The theoretical mechanism is straightforward: during an early cell division, chromosomes can lag behind or fail to separate properly. If the affected cell and the unaffected cell each go on to seed a separate twin, the result is two genetically identical individuals except for the missing or rearranged chromosome. One early analysis laid out how a normal XY zygote undergoing non-disjunction at the first cleavage could produce one cell line with an XO constitution and another with XYY or XXY, with subsequent chromosome losses potentially yielding twins of different apparent sex.{5PubMed Central. Monozygotic twins of different sex}
Sesquizygotic Twins, the “Semi-Identical” Category
In 2019, researchers reported a case that did not fit neatly into either the identical or the fraternal category. A pair of twins shared a single placenta, a hallmark of identical twinning, yet one was male and the other female. Genetic testing showed the twins were identical on their mother’s side but shared only about 78% of their father’s DNA. The explanation: a single egg was fertilized by two sperm simultaneously, and the resulting cell mass then divided into two embryos. The researchers called these twins sesquizygotic, a term meaning roughly “one-and-a-half zygotic.”6PubMed. Molecular Support for Heterogonesis Resulting in Sesquizygotic Twinning
The concept had actually been proposed years earlier as a theoretical possibility. In 2002, a hypothesis paper described how gene variants in fathers could increase the odds of an egg being fertilized by two sperm and the resulting embryo surviving, producing twins that would be an “exceptional intermediate” between identical and fraternal.{7Twin Research and Human Genetics. Paternal Familial Twinning: Hypothesis and Genetic/Medical Implications} The 2019 case was the first confirmed in a living pregnancy. Because each twin received a different mix of the two sperm’s chromosomes, one twin inherited two X chromosomes and the other got an X and a Y, resulting in a girl and a boy who are genetically somewhere between identical and fraternal twins.
Sesquizygotic twinning is vanishingly rare. The 2019 paper described it as the second confirmed case ever (the first was identified retrospectively in a different context). For practical purposes, a boy-girl pair sharing a placenta is still far more likely to be explained by the chromosomal-loss scenario or a monochorionic dizygotic pregnancy than by sesquizygosis, but the case proved that this in-between category genuinely exists.
Same Chromosomes, Different Apparent Sex
There is yet another scenario, subtler than the ones above. Two identical twins can carry the exact same sex chromosomes and still end up looking like different sexes. This happens through conditions known broadly as differences of sex development, where the body’s response to sex hormones diverges between the two twins despite identical DNA.
One documented case involved twins who were both 46,XY. One developed as a typical male. The other had complete androgen insensitivity syndrome (CAIS), meaning the body’s cells could not respond to testosterone. That twin developed female external anatomy despite having XY chromosomes. Physical examination of the male twin showed typical male features and palpable testes, while the other twin presented as female.{8PubMed Central. Complete androgen insensitivity syndrome in twins with discordant phenotypes: a case report and review of the literature} Another case described identical 46,XY twins where one was male with mixed gonadal dysgenesis and the other was female with gonadal dysgenesis. Genetic markers confirmed they were monozygotic, and the SRY gene (the gene that typically triggers male development) was present in both. The researchers proposed that the discordance could be explained by mutations or mosaicism in genes further downstream in the sex-determination pathway, or by cryptic cell lines missing the Y in the gonads of the affected twin.{9Cytogenetic and Genome Research. Monozygotic twins of opposite sex}
These cases are a reminder that chromosomal sex and physical sex are related but not identical concepts. Two people can share every letter of their DNA sequence and still end up on different developmental paths if a mutation occurs in a critical tissue at a critical time, or if random variation in gene expression tips the balance differently in each twin.
How Identical Twins Become Less Identical Over Time
Even when identical twins are unambiguously the same sex and appear highly similar, they are not perfect genetic copies. After the fertilized egg splits, every subsequent cell division carries a small chance of introducing a new mutation. These post-zygotic somatic mutations accumulate throughout life, driven by DNA replication errors, environmental exposures like UV light or cigarette smoke, and simple chance.{10DNA Research. Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins} One study sequencing the genomes of identical twins provided direct evidence that early somatic mutations occur and can create genetic differences between otherwise identical individuals, with mutations accumulating across the trillions of cell divisions over a lifetime.{11PubMed. Somatic point mutations occurring early in development: a monozygotic twin study}
On top of the DNA sequence itself, the way genes are switched on and off changes independently in each twin. A landmark study comparing identical twins across different ages found that young twins were nearly indistinguishable in their epigenetic profiles, but older twins showed striking differences in DNA methylation and histone modification patterns, which in turn affected which genes were active.{12PubMed Central. Epigenetic differences arise during the lifetime of monozygotic twins} This epigenetic drift helps explain why identical twins can diverge in traits like disease susceptibility, body composition, and even personality over time, without any dramatic chromosomal event.
Chimerism Adds Another Layer of Confusion
Sometimes twins who are clearly fraternal can share cells, which muddies genetic testing. When two embryos share a blood supply in the womb, blood-forming stem cells can migrate between them. The result is chimerism: each twin carries a mix of their own cells and their co-twin’s cells, at least in certain tissues. In one case of sex-discordant twins who shared a single placenta after double blastocyst transfer in an IVF cycle, postnatal genetic testing found mixed 46,XX and 46,XY cell lines in the twins’ blood, consistent with blood-limited chimerism.{13PubMed Central. Sex-Discordant Monochorionic Dizygotic Twins After Double Blastocyst Transfer: Blood Chimerism Demonstrated by Multimodal Genetic Testing}
Chimerism matters for two practical reasons. First, a blood test on one twin might return a result suggesting the twin carries both XX and XY chromosomes, which could be mistaken for a disorder of sex development when really the XX cells came from the co-twin. Second, chimerism can confuse zygosity testing. If you test blood from both twins and find they share certain genetic markers, you might conclude they are identical when they are actually fraternal twins who swapped some cells in utero. Reliable zygosity testing typically requires sampling a tissue that is less likely to be chimeric, such as cheek cells, along with multiple genetic markers.
How Zygosity Is Actually Determined
Parents of same-sex twins often wonder whether their children are identical or fraternal, and the answer is not always obvious from appearance. The gold standard is DNA testing. A validated approach uses a panel of about 50 single nucleotide polymorphisms, small points of genetic variation scattered across the genome, to determine with high reliability whether two individuals share the same DNA.{14PubMed. Large-scale zygosity testing using single nucleotide polymorphisms} If the twins match at every marker, they are identical. If they differ at multiple markers, they are fraternal.
For boy-girl pairs, this testing is almost never needed. Different sexes mean different sex chromosomes, which means two separate fertilization events, which means fraternal. The only reason to test further would be clinical signs suggesting one of the rare scenarios described above, such as a shared placenta in a boy-girl pair, or features of Turner syndrome or a sex-development condition in one twin. In the absence of those red flags, a boy-girl pair can be confidently called fraternal.
IVF and the Rate of Identical Twinning
Couples who conceive through assisted reproduction sometimes face a slightly elevated chance of a single transferred embryo splitting into identical twins. A systematic review estimated that the rate of monozygotic twinning after assisted conception is about 0.9%, compared to roughly 0.4% in natural conception, representing at least a two-fold increase.{15Human Reproduction Update. The risk of monozygotic twins after assisted reproductive technology: a systematic review and meta-analysis} The risk appears to be particularly tied to blastocyst-stage transfers, where embryos are cultured for five days before being placed in the uterus. In one large multicentre study, the rate of monozygotic twinning was about six times higher after blastocyst transfer than after earlier-stage embryo transfer.{16PubMed Central. Odds and Predictors of Monozygotic Twinning in a Multicentre Cohort of 25,794 IVF Cycles}
Another study found that higher maternal age was associated with a slightly increased risk of the embryo splitting, while frozen embryo transfers appeared to be somewhat protective compared to fresh transfers.{17Human Reproduction Open. Risk factors associated with monozygotic twinning in offspring conceived by assisted reproductive technology} These findings matter because monozygotic twin pregnancies carry higher risks than dizygotic ones, including complications from shared placentas. They also mean that even when a single embryo is transferred to avoid twins, a monozygotic split can still produce a twin pregnancy, and that twin pair will always be the same sex under normal circumstances.
Why Same-Sex Pairs Are More Common Among Fraternal Twins
If fraternal twins are formed by two independent fertilizations each with a 50-50 shot at producing a boy or a girl, you might expect the split between same-sex and opposite-sex pairs to be roughly even. In practice, same-sex fraternal pairs slightly outnumber opposite-sex pairs. In UK data, the proportion of same-sex pairs among dizygotic twins was about 60%, significantly higher than the expected baseline. US data showed a similar skew, with same-sex pairs making up about 57%.{18Human Reproduction. Why are there more same-sex than opposite-sex dizygotic twins?} Several mechanisms have been proposed for this excess, including differential survival of same-sex versus opposite-sex pairs in utero and hormonal factors that could influence whether the second egg released is fertilized by a sperm of the same or different sex chromosome type. The practical takeaway is that parents of boy-girl twins are in the minority among all twin parents, and are nearly certain to have fraternal twins.
Telling Identical Twins Apart in Forensics
Standard forensic DNA profiling cannot distinguish between identical twins. The short tandem repeat markers used in criminal and paternity cases are inherited, not acquired, so both twins produce the same profile.{19PubMed. Monozygotic twins: Identical or distinguishable for science and law?} This has created real legal problems. If DNA at a crime scene matches both twins, the evidence alone cannot pinpoint which one was there.
Researchers have developed a workaround using ultra-deep sequencing to detect the rare somatic mutations that distinguish one twin from the other. Because these mutations are unique to each twin’s cell lineages, they can serve as a genetic fingerprint that separates two otherwise indistinguishable genomes.{20PubMed. Finding the needle in the haystack: differentiating “identical” twins in paternity testing and forensics by ultra-deep next generation sequencing} The technique is expensive and not yet routine, but it has been used successfully in paternity disputes and criminal investigations. In one documented twin pair discordant for a psychiatric condition, validated somatic mutations were found at allele fractions between roughly 1% and 7%, meaning the mutations were present in only a small fraction of cells but were still detectable.{21PubMed Central. Identification of somatic mutations in monozygotic twins discordant for psychiatric disorders}
Identical Twinning in Other Species
Monozygotic twinning is uncommon in most mammals, but it is the norm in at least one. The nine-banded armadillo routinely produces monozygotic quadruplets: a single fertilized egg splits twice, yielding four genetically identical offspring every time. Research has noted the parallel between the armadillo’s embryonic splitting process and what happens in rare human monozygotic pregnancies, where a fertilized egg can also undergo two rounds of binary division.{22Twin Research and Human Genetics. On the Possible Cause of Monozygotic Twinning: Lessons From the 9-Banded Armadillo and From Assisted Reproduction} The armadillo’s obligate twinning suggests that whatever molecular trigger causes the embryo to split is not a random accident in that species but an evolved reproductive strategy. In humans, the trigger remains poorly understood, which is part of why identical twinning rates have stayed fairly stable across populations and generations while fraternal twinning rates fluctuate with factors like maternal age and fertility treatments.
Gender Identity in Twin Pairs
A separate question from biological sex is gender identity, and twin studies have been used to investigate whether it has a heritable component. A pooled analysis of over 460 twin pairs found that identical twins were far more likely to share a transgender or gender-diverse identity than fraternal twins. About 21% of identical twin pairs in the sample were concordant, compared to about 9% of fraternal pairs.{23PubMed Central. Using twin data to examine heritable and intrauterine hormonal influences on transgender and gender diverse identities} The higher concordance in identical twins, who share all their DNA, compared to fraternal twins, who share about half, points to a substantial genetic influence on gender identity. This finding is separate from the chromosomal and developmental scenarios that produce twins of different biological sex, but it underscores a broader point: even in pairs with the same genetic blueprint, the relationship between chromosomes, hormones, anatomy, and identity is not as simple as one gene, one outcome.