The prevalence of uterine malformation is estimated to be 6.7% in the general population, slightly higher (7.3%) in the infertility population, and significantly higher in a population of women with a history of recurrent miscarriages (16%).

In the United States, uterus didelphys is reported to occur in 0.1–0.5% of women. It is difficult to know the exact occurrence of this anomaly, as it may go undetected in the absence of medical and reproductive complications.

Most studies are based on populations of women who have experienced a pregnancy loss and thus do not address the issue of the prevalence in the general population. A screening study by Woelfer et al. of women without a history of reproductive problems found that about 3% of women had a uterine septation; the most common anomaly in their study was an arcuate uterus (5%), while 0.5% were found to have a bicornuate uterus. In contrast, in about 15% of patients with recurrent pregnancy loss anatomical problems are thought to be causative with the septate uterus as the most common finding.

A number of twin gestations have occurred where each uterus carried its pregnancy separately. A recent example occurred on February 26, 2009, when Sarah Reinfelder of Sault Ste. Marie, Michigan delivered two healthy, although seven weeks premature, infants by cesarean section at Marquette General Hospital. It is possible that the deliveries occur at different times, thus the delivery interval could be days or even weeks.

Cervical agenesis is estimated to occur in 1 in 80,000 females. It is often associated with deformity of the vagina; one study found that 48% of patients with cervical agenesis had a normal, functional vagina, while the rest of the cases were accompanied by vaginal hypoplasia.

The condition may not be known to the affected individual and not result in any reproductive problems; thus normal pregnancies may occur. However, it is associated with a higher risk for miscarriage, premature birth, and malpresentation. According to the classical study by Buttram there is a 60% risk of a spontaneous abortion, this being more common in the second than in the first trimester. However, there is no agreement on this number and other studies show a lower risk. Woelfer found that the miscarriage risk is more pronounced in the first trimester.

The condition is also associated with abnormalities of the renal system. Further, skeletal abnormalities have been linked to the condition.

Vaginal hypoplasia is estimated to occur in 1 in 4,000–5,000 live female births. It is often unnoticed until adolescence when pain and a lack of menstrual flow indicates the condition.

Fraser syndrome is a disorder that affects the development of the child prior to birth. Infants born with Fraser syndrome often have eyes that are malformed and completely covered by skin. Also the child is born with fingers and toes that are fused together along with abnormalities within the urine tract. As this disorder relates to vaginal atresia, infants born with Fraser syndrome are also born with malformations in their genitals.

A uterine malformation is a type of female genital malformation resulting from an abnormal development of the Müllerian duct(s) during embryogenesis. Symptoms range from amenorrhea, infertility, recurrent pregnancy loss, and pain, to normal functioning depending on the nature of the defect.

The prognosis for vaginal atresia is one that is complicated. There are variations in patients' anatomic findings as well as an absence in consistent surgical techniques which makes it difficult to give a prognosis for this condition. Along with other conditions that give rise to an abnormal perineum (i.e. ambiguous genitalia and other various abnormalities that range from cloaca to urogenital sinus), individuals with vaginal atresia often report reconstruction as an outcome of treatment. Due to this, it is difficult to compare outcomes between individuals with vaginal atresia.

Müllerian agenesis or müllerian aplasia, Mayer–Rokitansky–Küster–Hauser syndrome, or vaginal agenesis is a congenital malformation characterized by a failure of the Müllerian duct to develop, resulting in a missing uterus and variable degrees of vaginal hypoplasia of its upper portion. Müllerian agenesis (including absence of the uterus, cervix and/or vagina) is the cause in 15% of cases of primary amenorrhoea. Because most of the vagina does not develop from the Müllerian duct, instead developing from the urogenital sinus along with the bladder and urethra, it is present even when the Müllerian duct is completely absent.

Because ovaries do not develop from the Müllerian ducts, affected women might have normal secondary sexual characteristics but are infertile due to the lack of a functional uterus. However, motherhood is possible through use of gestational surrogates. Mayer-Rokitansky-Küster-Hauser syndrome (MRKH) is hypothesized to be a result of autosomal dominant inheritance with incomplete penetrance and variable expressivity, which contributes to the complexity involved in identifying of the underlying mechanisms causing the condition. Because of the variance in inheritance, penetrance and expressivity patterns, MRKH is subdivided into two types: type 1, in which only the structures developing from the Müllerian duct are affected (the upper vagina, cervix, and uterus), and type 2, where the same structures are affected, but is characterized by the additional malformations of other body systems most often including the renal and skeletal systems. MRKH type 2 includes MURCS (Müllerian Renal Cervical Somite). The majority of MRKH syndrome cases are characterized as sporadic, but familial cases have provided evidence that, at least for some patients, MRKH is an inherited disorder. The underlying causes of MRKH syndrome is still being investigated, but several causative genes have been studied for their possible association with the syndrome. Most of these studies have served to rule-out genes as causative factors in MRKH, but thus far, only WNT4 has been associated with MRKH with hyperandrogenism.

The medical eponym honors August Franz Josef Karl Mayer (1787–1865), Carl Freiherr von Rokitansky (1804–1878), Hermann Küster (1879–1964), and Georges Andre Hauser (1921–2009).

WNT4 (found on the short arm (p) of chromosome 1) has been clearly implicated in the atypical version of this disorder. A genetic mutation causes a leucine to proline residue substitution at amino acid position 12. This occurrence reduces the intranuclear levels of β catenin. In addition, it removes the inhibition of steroidogenic enzymes like 3β-hydroxysteriod dehydrogenase and 17α-hydroxylase. Patients therefore have androgen excess. Furthermore, without WNT4, the Müllerian duct is either deformed or absent. Female reproductive organs, such as the cervix, fallopian tubes, ovaries, and much of the vagina, are hence affected.

An association with a deletion mutation in the long arm (q) of chromosome 17 (17q12) has been reported. The gene LHX1 is located in this region and may be the cause of a number of these cases.

Vaginal hypoplasia is the underdevelopment or incomplete development of the vagina. It is a birth defect or congenital abnormality of the female genitourinary system.

Cervical agenesis is a congenital disorder of the female genital system that manifests itself in the absence of a cervix, the connecting structure between the uterus and vagina. Milder forms of the condition, in which the cervix is present but deformed and nonfunctional, are known as cervical atresia or cervical dysgenesis.

Diets high in fruits and vegetables tend to lower the risk of developing fibroids. Fruits, especially citrus, have a greater protective benefit than vegetables. Normal dietary levels of vitamin D is shown to reduce the risk of developing fibroids. No protective benefit has been found with the consumption of folate, whole grains, soy products, or fiber. No association between the consumption of fat, eggs, dairy products has been shown to increase the risk of fibroids.

It is a rare condition, with only approximately 60 cases reported as of 1989, and 75 cases as of 2005. However, due to the stigma of intersex conditions and the issues of keeping accurate statistics and records among doctors, it is likely there are more cases than reported.

Individuals with CAVD can reproduce with the assistance of modern technology with a combination of testicular sperm extraction and intracytoplasmic sperm injection (ICSI). However, as the risk of either cystic fibrosis or renal agenesis is likely to be higher in the children, genetic counseling is generally recommended.

Some risk factors associated with the development of uterine fibroids are modifiable.

Fibroids are more common in obese women. Fibroids are dependent on estrogen and progesterone to grow and therefore relevant only during the reproductive years.

Aphallia has no known cause. It is not linked to deficient hormone amounts or action, but rather to a failure of the fetal genital tubercle to form between 3 and 6 weeks after conception. The urethra of an affected child opens on the perineum.

There are two main populations of CAVD; the larger group is associated with

cystic fibrosis and occurs because of a mutation in the CFTR gene, while the smaller group (estimated between 10 and 40%) is associated with Unilateral Renal agenesis (URA). The genetic basis of this second group is not well understood.

Mutation of the CFTR gene is found to result in obstructive azoospermia in postpubertal males with cystic fibrosis. Strikingly, CAVD is one of the most consistent features of cystic fibrosis as it affects 98-99% of individuals in this CF patient population. In contrast, acute or persistent respiratory symptoms present in only 51% of total CF patients.

In the subset of males with both CBAVD and URA, the CFTR mutation has been shown to occur at a rate only slightly higher than the overall population. Thus, McCallum, et al. have suggested another mutation may be responsible for this condition.

Many factors can contribute to the loss of uterine muscle tone, including:

- overdistention of the uterus

- multiple gestations

- polyhydramnios

- fetal macrosomia

- prolonged labor

- oxytocin augmentation of labor

- grand multiparity (having given birth 5 or more times)

- precipitous labor (labor lasting less than 3 hours)

- magnesium sulfate treatment of preeclampsia

- chorioamnionitis

- halogenated anesthetics

- uterine leiomyomata

- full bladder

- retained colyledon, placental fragments

- placenta previa

- placental abruption

- constriction ring

- incomplete separation of the placenta

In an embryo, the conversion of the gonads into testicles in males-to-be and into ovaries in females-to-be is the function of Leydig cells. In testicular agenesis, this process fails. Penile agenesis can be caused by testicular agenesis. Testes are the sole producer of 5-alpha dihydrotestosterone (5aDHT) in the male body. Where the gonads fail to metamorphose into testes, there is no 5aDHT. Therefore, the masculising process that builds the genital tubercle, the precursor to the penis, is stillborn. When this happens, the child is born with both penile and testicular agenesis and is known by the slang term "nullo". This combination of both conditions is estimated to occur in between 20-30 million male births.

Penile agenesis can exist independently after full testicular development; in this case its cause is unknown.

Penile agenesis is a birth defect in humans, occurring about once in 5–6 million male births, in which a male child is born without a penis.

A partner condition is testicular or gonadal agenesis. This is when a male child is born without gonads and consequently develops no testes. Penile agenesis occurs often as a consequence of Testicular agenesis, but the reverse is never the case. Most patients in both cases have no known family history and usually have an otherwise normal male anatomy.

Michels Caskey syndrome is a rare disorder that combines spinal and skeletal abnormalities, especially of the thumbs, with abnormal or absent female reproductive organs. Examples include the absence of a cervix and upper vagina or abnormalities of the uterus or vagina. Symptoms may also include scoliosis and primary amenorrhea. Synonyms include Mullerian aplasia with hypoplastic thumbs, hypoplastic thumb Mullerian aplasia, and Mullerian aplasia with unilateral hypoplasia of the thumbs and skeletal spine deformities.

In medicine, agenesis () refers to the failure of an organ to develop during embryonic growth and development due to the absence of primordial tissue. Many forms of agenesis are referred to by individual names, depending on the organ affected:

- Agenesis of the corpus callosum - failure of the Corpus callosum to develop

- Renal agenesis - failure of one or both of the kidneys to develop

- Phocomelia - failure of the arms or legs to develop

- Penile agenesis - failure of penis to develop

- Müllerian agenesis - failure of the uterus and part of the vagina to develop

- Agenesis of the gallbladder - failure of the Gallbladder to develop. A person may not realize they have this condition unless they undergo surgery or medical imaging, since the gallbladder is neither externally visible nor essential.