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.

Persistent Müllerian duct syndrome (PMDS) is the presence of Müllerian duct derivatives (fallopian tubes, uterus, and/or the upper part of the vagina) in what would be considered a genetically and otherwise physically normal male animal by typical human based standards. In humans, PMDS typically is due to an autosomal recessive congenital disorder and is considered by some to be a form of pseudohermaphroditism due to the presence of Müllerian derivatives.

Typical features include undescended testes (cryptorchidism) and the presence of a small, underdeveloped uterus in an XY infant or adult. This condition is usually caused by deficiency of fetal anti-Müllerian hormone (AMH) effect due to mutations of the gene for AMH or the anti-Müllerian hormone receptor, but may also be as a result of insensitivity to AMH of the target organ.

PMDS type I results from mutations of the gene ("AMH") for AMH on chromosome 19p3.3.

PMDS type II results from mutations of the gene ("AMH-RII") for the AMH receptor on 12q13.

Both types of disorders are inherited as autosomal recessive conditions with expression usually limited to XY offspring.

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%).

When an infant is born with PSH, the most difficult management decision has often been the sex assignment, since genitalia with this degree of ambiguity do not resemble either sex very well with respect to looks or function. Many infants with PPHS have been assigned and raised as female despite presence of testes and XY chromosomes.

Nearly all parents of infants with PPSH are offered surgical reconstruction, to either further masculinize or feminize the external genitalia.

Treatment with testosterone postnatally does not close the urethra or change the malformation, but in some cases may enlarge the penis slightly.

Bardet-Biedl syndrome (BBS) is a cliopathic human genetic disorder that can affect various parts of the body. Parts of the urogenital system where the effects of BBS are seen include: ectopic urethra, renal failure, uterus duplex, hypogonadism, septate vagina, and hypoplasia of the fallopian tubes, uterus, ovaries. Some of the common characteristics associated with this syndrome include intellectual disorders, loss of vision, kidney problems, and obesity.

The mechanism that causes BBS is still remains unclear. Mutations in more than 20 genes can cause BBS and is an inherited recessive condition. Some of the gene mutations that occur in BBS are listed below:

"BBS1, BBS2, ARL6 (BBS3), BBS4, BBS5, MKKS (BBS6), BBS7, TTC8 (BBS8), BBS9, BBS10, TRIM32 (BBS11), BBS12, MKS1 (BBS13), CEP290 (BBS14), WDPCP (BBS15), SDCCAG8 (BBS16), LZTFL1 (BBS17), BBIP1 (BBS18), IFT27 (BBS19), IFT72 (BBS20)", and "C8ORF37(BBS21") The majority of the genes that are related to BBS encode proteins which are called cilia and basal bodies, which are related structures.

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.

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).

It is considered a form of 5-alpha-reductase deficiency involving SRD5A2.

During embryogenesis, without any external influences for or against, the human reproductive system is intrinsically conditioned to give rise to a female reproductive organisation.

As a result, if a gonad cannot express its sexual identity via its hormones—as in gonadal dysgenesis—then the affected person, no matter whether their chromosomes are XY or XX, will develop external female genitalia. Internal female genitalia, primarily the uterus, may or may not be present depending on the cause of the disorder.

In both sexes, the commencement and progression of puberty require functional gonads that will work in harmony with the hypothalamic and pituitary glands to produce adequate hormones.

For this reason, in gonadal dysgenesis the accompanying hormonal failure also prevents the development of secondary sex characteristics in either sex, resulting in a sexually infantile female appearance and infertility.

Individuals with CAIS are raised as females. They are born phenotypically female and almost always have a heterosexual female gender identity; the incidence of homosexuality in women with CAIS is thought to be less than unaffected women. However, at least two case studies have reported male gender identity in individuals with CAIS.

This condition will occur if there is an absence of both Müllerian inhibiting factor and testosterone. The absence of testosterone will result in regression of the Wolffian ducts; normal male internal reproductive tracts will not develop. The absence of Müllerian inhibiting factor will allow the Müllerian ducts to differentiate into the oviducts and uterus. In sum, this individual will possess female-like internal and external reproductive characteristics, lacking secondary sex characteristics. The genotype may be either 45,XO, 46,XX or 46,XY.

Eye agenesis is a medical condition in which people are born with no eyes.

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.

If both ejaculatory ducts are completely obstructed, affected men will demonstrate male infertility due to aspermia/azoospermia. They will suffer from a very low volume of semen which lacks the gel-like fluid of the seminal vesicles or from no semen at all while they are able to have the sensation of an orgasm during which they will have involuntary contractions of the pelvic musculature. This is contrary to some other forms of anejaculation.

Ejaculatory duct obstruction is the underlying cause for 1–5% of male infertility.

In addition, it is reported to be a cause for pelvic pain, especially shortly after ejaculation. In case of proven fertility but unresolved pelvic pain, even one or both partially obstructed ejaculatory ducts may be the origin of pelvic pain and oligospermia.

Ejaculatory duct obstruction may result in a complete lack of semen (aspermia) or a very low-volume semen (oligospermia) which may contain only the secretion of accessory prostate glands downstream to the orifice of the ejaculatory ducts.

In addition to the congenital form which is often caused by cysts of the müllerian duct the obstruction can be acquired due to an inflammation caused by chlamydia, prostatitis, tuberculosis of the prostate and other pathogens. In Addition, calculus was reported to mechanically block the ejaculatory duct, leading to infertility. However, in many patients, there is no history of an inflammation and the underlying cause simply remains unknown.

Ejaculatory duct obstruction (EDO) is a congenital or acquired pathological condition which is characterized by the obstruction of one or both ejaculatory ducts. Thus, the efflux of (most constituents of) semen is not possible.

It is a cause of male infertility and / or pelvic pain. Ejaculatory duct obstruction must not be confused with an obstruction of the vas deferens.

Challenges presented to people affected by this condition include: psychologically coming to terms with the condition, difficulties with sexual function, infertility. Long-term studies indicate that with appropriate medical and psychological treatment, women with CAIS can be satisfied with their sexual function and psychosexual development. CAIS women can lead active lives and expect a normal lifespan.

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.

MURCS association (a variant of Mayer-Rokitansky-Küster-Hauser syndrome) is a very rare developmental disorder that primarily affects the reproductive and urinary systems involving MUllerian agenesis, Renal agenesis, Cervicothoracic Somite abnormalities. It affects only females.

Treatment includes androgen (testosterone) supplementation to artificially initiate puberty, testicular prosthetic implantation, and psychological support. Gender Dysphoria may result in anorchic individuals who are assigned male at birth and raised as male despite lacking the necessary masculinizing hormones during prenatal, childhood, and adolescent development. Anorchic individuals who have a female identity may be administered estrogen alone in place of testosterone as no androgen blockers are necessary due to the lack of gonads.

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.

Sertoli cell only syndrome is like other non-obstructive azoospermia (NOA) cases are managed by sperm retrieval through testicular sperm extraction (mTESE), micro-surgical testicular sperm extraction (mTESE), or testicular biopsy. On retrieval of viable sperm this could be used in Intracytoplasmic Sperm injection ICSI

In 1979, Levin described germinal cell aplasia with focal spermatogenesis where a variable percentage of seminiferous tubules contain germ cells. It is important to discriminate between both in view of ICSI.

A retrospective analysis performed in 2015 detailed the outcomes of N=148 men with non-obstructive azoospermia and diagnosed Sertoli cell-only syndrome:

- Men with SCOS: 148

- Testicular sperm was successfully retrieved: 35/148

- Successful ICSI: 20/148

- Clinical pregnancy: 4/148

This study considers the effect of FSH levels on clinical success, and it excludes abnormal karyotypes. All patients underwent MD-TESE in Iran. Ethnicity and genetic lineage may have an impact on treatment of azoospermia [citation needed].

Sertoli cell-only syndrome (a.k.a. Del Castillo syndrome and germ cell aplasia ) is a disorder characterized by male sterility without sexual abnormality. It describes a condition of the testes in which only Sertoli cells line the seminiferous tubules.

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.