Because both the Wolffian ducts and Müllerian ducts begin to develop, the tissues are often intertwined, resulting in obstruction or nonpatency of the vas deferens or other parts of the reproductive excretory ducts. This can result in infertility, the most serious potential problem caused by this condition. Sometimes, transverse testicular ectopia is evident.

Cryptorchidism in AMH deficiency suggests that AMH may play a role in transabdominal testicular descent, perhaps by facilitating contraction of the gubernaculum.

Other Müllerian derivatives which may be present in at least a rudimentary form are the cervix, upper part of the vagina, and fallopian tubes.

The condition can come to attention because of a bulge in the inguinal canal of an XY infant due to herniation of the uterus. The presence of a uterus may be noticed if an ultrasound or MRI of the pelvis is performed to locate the testes or for other reasons. Occasionally the uterus is discovered during abdominal surgery for some other purpose in later childhood or adult life.

Although persistent Müllerian duct syndrome is classified as an intersex condition, it does not involve ambiguity or malformation of the external genitalia, which appear typical (apart from cryptorchidism if present). Sometimes the uterus enters a hernia. Sometimes the Müllerian structures get entangled with the spermatic ducts and interfere with the descent of the testes.

Apart from humans, this syndrome has been reported in dogs.

Symptoms and signs in the newborn can be sepsis, abdominal mass, and respiratory distress. Other abdominopelvic or perineal congenital anomalies frequently prompt radiographic evaluation in the newborn, resulting in a diagnosis of coincident vaginal atresia. Symptoms for vaginal atresia include cyclical abdominal pain, the inability to start having menstrual cycles, a small pouch or dimple where a vaginal opening should be, and pelvic mass when the upper vagina becomes filled with menstrual blood. Signs and symptoms of vaginal atresia or vaginal agenesis can often go unnoticed in females until they reach the age of menstruation. Women may also experience some form of abdominal pain or cramping.

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.

Vaginal hypoplasia can vary in severity from being smaller than normal to being completely absent.

Vaginal atresia can sometimes be diagnosed by physical examination soon after birth. A child with vaginal atresia often has other congenital abnormalities and other tests such as x-ray and tests to evaluate the kidney are done. Findings in adolescents may include abdominal pain, difficulty voiding, and backache, but most present with amenorrhea. Difficulties with sexual intercourse can suggest atresia. In the event that the condition is not caught shortly after birth, vaginal atresia becomes more evident when no menstrual cycle is occurs. If vaginal atresia is suspected by the doctor, a blood test may also be request for any of the previously mentioned syndromes, a magnetic resonance imaging (MRI) test, or an ultrasound. A regular evaluation of children born with an imperforate anus or anorectal malformation should be paired with the assessment of the results from these tests.

The absence of a vagina is a result of vaginal agenesis. Diagnostically, it may look similar to a vaginal obstruction such as can be caused by an imperforate hymen or, less commonly, a transverse vaginal septum.

It is frequently associated with Mayer-Rokitansky-Küstner-Hauser (MRKH) syndrome, in which the most common result is an absent uterus in conjunction with a deformed or missing vagina, despite the presence of normal ovaries and normal external genitalia. It is also associated with cervical agenesis, in which the uterus is present but the uterine cervix is absent.

The situation is most urgent where there is a menstruating uterus with an obstructed uterovaginal outflow, leading to hematometra. In this case prompt medical action is required.

An individual with this condition is hormonally normal; that is, the person will enter puberty with development of secondary sexual characteristics including thelarche and adrenarche (pubic hair). The person's chromosome constellation will be 46,XX. At least one ovary is intact, if not both, and ovulation usually occurs. Typically, the vagina is shortened and intercourse may, in some cases, be difficult and painful. Medical examination supported by gynecologic ultrasonography demonstrates a complete or partial absence of the cervix, uterus, and vagina.

If there is no uterus, a person with MRKH cannot carry a pregnancy without intervention. It is possible for the person to have genetic offspring by in vitro fertilization (IVF) and surrogacy. Successful uterine transplant has been performed in limited numbers of patients, resulting in several live births, but the technique is not widespread or accessible to many women.

A person with MRKH typically discovers the condition when, during puberty years, the menstrual cycle does not start (primary amenorrhoea). Some find out earlier through surgeries for other conditions, such as a hernia.

The American Fertility Society (now American Society of Reproductive Medicine) Classification distinguishes:

- Class I: Müllerian agenesis (absent uterus).

- Uterus is not present, vagina only rudimentary or absent. The condition is also called Mayer-Rokitansky-Kuster-Hauser syndrome. The patient with MRKH syndrome will have primary amenorrhea.

- Class II: Unicornuate uterus (a one-sided uterus).

- Only one side of the Müllerian duct forms. The uterus has a typical "banana shape" on imaging systems.

- Class III: Uterus didelphys, also uterus didelphis (double uterus).

- Both Müllerian ducts develop but fail to fuse, thus the patient has a "double uterus". This may be a condition with a double cervix and a vaginal partition (v.i.), or the lower Müllerian system fused into its unpaired condition. See Triplet-birth with Uterus didelphys for a case of a woman having spontaneous birth in both wombs with twins.

- Class IV: Bicornuate uterus (uterus with two horns).

- Only the upper part of that part of the Müllerian system that forms the uterus fails to fuse, thus the caudal part of the uterus is normal, the cranial part is bifurcated. The uterus is "heart-shaped".

- Class V: Septated uterus (uterine septum or partition).

- The two Müllerian ducts have fused, but the partition between them is still present, splitting the system into two parts. With a complete septum the vagina, cervix and the uterus can be partitioned. Usually the septum affects only the cranial part of the uterus. A uterine septum is the most common uterine malformation and a cause for miscarriages. It is diagnosed by medical image techniques, i.e. ultrasound or an MRI. MRI is considered the preferred modality due to its multiplanar capabilities as well as its ability to evaluate the uterine contour, junctional zone, and other pelvic anatomy. A hysterosalpingogram is not considered as useful due to the inability of the technique to evaluate the exterior contour of the uterus and distinguish between a bicornuate and septate uterus.

A uterine septum can be corrected by hysteroscopic surgery.

- Class VI: DES uterus.

- The uterine cavity has a "T-shape" as a result of fetal exposure to diethylstilbestrol.

An additional variation is the arcuate uterus where there is a concave dimple in the uterine fundus within the cavity.

A rudimentary uterus is a uterine remnant not connected to cervix and vagina and may be found on the other side of an unicornuate uterus.

Patients with uterine abnormalities may have associated renal abnormalities including unilateral renal agenesis.

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.

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).

Cryptorchidism is the absence of one or both testes from the scrotum. It is the most common birth defect of the male genital. About 3% of full-term and 30% of premature infant boys are born with at least one undescended testis. However, about 80% of cryptorchid testes descend by the first year of life (the majority within three months), making the true incidence of cryptorchidism around 1% overall. Cryptorchidism may develop after infancy, sometimes as late as young adulthood, but that is exceptional.

Cryptorchidism is distinct from monorchism, the condition of having only one testicle. The condition may occur on one or both sides; it more commonly affects the right testis.

A testis absent from the normal scrotal position may be:

1. anywhere along the "path of descent" from high in the posterior (retroperitoneal) abdomen, just below the kidney, to the inguinal ring;

2. in the inguinal canal;

3. "ectopic", having "wandered" from the path of descent, usually outside the inguinal canal and sometimes even under the skin of the thigh, the perineum, the opposite scrotum, or the femoral canal;

4. undeveloped ("hypoplastic") or severely abnormal ("dysgenetic");

5. missing (also see anorchia).

About two-thirds of cases without other abnormalities are unilateral; most of the other third involve both testes. In 90% of cases an undescended testis can be felt in the inguinal canal. In a small minority of cases missing testes may be found in the abdomen or appear to be nonexistent (truly "hidden").

Undescended testes are associated with reduced fertility, increased risk of testicular germ cell tumors and psychological problems when the boy is grown. Undescended testes are also more susceptible to testicular torsion (and subsequent infarction) and inguinal hernias. Without intervention, an undescended testicle will usually descend during the first year of life, but to reduce these risks, undescended testes can be brought into the scrotum in infancy by a surgical procedure called an orchiopexy.

Although cryptorchidism nearly always refers to "congenital" absence or maldescent, a testis observed in the scrotum in early infancy can occasionally "reascend" (move back up) into the inguinal canal. A testis which can readily move or be moved between the scrotum and canal is referred to as "retractile". The word is from the Greek "κρυπτός", "kryptos", meaning hidden "ὄρχις", "orchis", meaning testicle.

Cryptorchidism, hypospadias, testicular cancer and poor semen quality make up the syndrome known as testicular dysgenesis syndrome.

Many men who were born with undescended testes have reduced fertility, even after orchiopexy in infancy. The reduction with unilateral cryptorchidism is subtle, with a reported infertility rate of about 10%, compared with about 6% reported by the same study for the general population of adult men.

The fertility reduction after orchiopexy for bilateral cryptorchidism is more marked, about 38%, or 6 times that of the general population. The basis for the universal recommendation for early surgery is research showing degeneration of spermatogenic tissue and reduced spermatogonia counts after the second year of life in undescended testes. The degree to which this is prevented or improved by early orchiopexy is still uncertain.

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.

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

A bicornuate uterus or bicornate uterus (from the Latin "cornū", meaning "horn"), commonly referred to as a "heart-shaped" uterus, is a uterus composed of two "horns" separated by a septum. In humans, a bicornuate uterus is a type of uterine malformation, but in some other mammalian species, including rodents and pigs, it is normal.

Sertoli cell only syndrome is likely multifactorial, and characterized by severely reduced or absent spermatogenesis despite the presence of both Sertoli and Leydig cells. A substantial subset of men with this uncommon syndrome have microdeletions in the Yq11 region of the Y chromosome, an area known as the AZF (azoospermia factor) region. Generally speaking, testosterone and LH levels are normal, but due to lack of inhibin, FSH levels are increased.

The Sertoli cell-only syndrome patients normally have normal secondary male features and have normal- or small-sized testes.

A unicornuate uterus represents a uterine malformation where the uterus is formed from one only of the paired Müllerian ducts while the other Müllerian duct does not develop or only in a rudimentary fashion. The sometimes called "hemi-uterus" has a single horn linked to the ipsilateral fallopian tube that faces its ovary.

A uterine septum is a form of a congenital malformation where the uterine cavity is partitioned by a longitudinal septum; the outside of the uterus has a normal typical shape. The wedge-like partition may involve only the superior part of the cavity resulting in an "incomplete septum" or a "subseptate uterus", or less frequently the total length of the cavity ("complete septum") and the cervix resulting in a double cervix. The septation may also continue caudally into the vagina resulting in a "double vagina".

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.

The condition may be due to:

- Turner syndrome, and its variations (i.e. mosaicism)

- XX gonadal dysgenesis, also pure gonadal dysgenesis, 46,XX

- Swyer syndrome, also pure gonadal dysgenesis, 46,XY

- Perrault syndrome, XX gonadal dysgenesis + sensorineural hearing loss

- Mixed gonadal dysgenesis

- Exposure to environmental endocrine disruptors

Gonadal dysgenesis is any congenital developmental disorder of the reproductive system characterized by a progressive loss of germ cells on the developing gonads of an embryo. This loss leads to extremely hypoplastic (underdeveloped) and dysfunctioning gonads mainly composed of fibrous tissue, hence the name streak gonads—i.e., a form of aplasia in which the ovary is replaced by functionless tissue. The accompanying hormonal failure also prevents the development of secondary sex characteristics in either sex, resulting in a sexually infantile female appearance and infertility.

The first type of gonadal dysgenesis discovered was Turner syndrome.

It is possible to diagnose a bicornuate uterus using gynecologic ultrasonography, specifically sonohysterography, and MRI. However, as there is no indication to do such procedures on asymptomatic women, the presence of a bicornuate uterus may not be detected until pregnancy or delivery.

In a C-section (usually done due to malpresentation), the irregular shape of the uterus will be apparent.

Other less reliable diagnostic imaging methods include hysterosalpingography and hysteroscopy; these procedures are typically done during the course of an infertility investigation.

A vaginal septum is a congenital partition within the vagina; such a septum could be either longitudinal or transverse.

Individuals with complete androgen insensitivity syndrome (grades 6 and 7 on the Quigley scale) are born phenotypically female, without any signs of genital masculinization, despite having a 46,XY karyotype. Symptoms of CAIS do not appear until puberty, which may be slightly delayed, but is otherwise normal except for absent menses and diminished or absent secondary terminal hair. Axillary hair (i.e. armpit hair) fails to develop in one third of all cases. External genitalia is normal, although the labia and clitoris are sometimes underdeveloped. The vaginal depth varies widely, but is typically shorter than unaffected women; one study of eight women with CAIS measured the average vaginal depth to be 5.9 cm (vs. 11.1 ± 1.0 cm for unaffected women ). In some extreme cases, the vagina has been reported to be aplastic (resembling a "dimple"), though the exact incidence of this is unknown.

The gonads in these women are not ovaries, but instead, are testes; during the embryonic stage of development, testes form in an androgen-independent process that occurs due to the influence of the SRY gene on the Y chromosome. They may be located intra-abdominally, at the internal inguinal ring, or may herniate into the labia majora, often leading to the discovery of the condition. Testes in affected women have been found to be atrophic upon gonadectomy. Testosterone produced by the testes cannot be directly used due to the mutant androgen receptor that characterizes CAIS; instead, it is aromatized into estrogen, which effectively feminizes the body and accounts for the normal female phenotype observed in CAIS.

Immature sperm cells in the testes do not mature past an early stage, as sensitivity to androgens is required in order for spermatogenesis to complete. Germ cell malignancy risk, once thought to be relatively high, is now thought to be approximately 2%. Wolffian structures (the epididymides, vasa deferentia, and seminal vesicles) are typically absent, but will develop at least partially in approximately 30% of cases, depending on which mutation is causing the CAIS. The prostate, like the external male genitalia, cannot masculinize in the absence of androgen receptor function, and thus remains in the female form.

The Müllerian system (the fallopian tubes, uterus, and upper portion of the vagina) typically regresses due to the presence of anti-Müllerian hormone originating from the Sertoli cells of the testes. These women are thus born without fallopian tubes, a cervix, or a uterus, and the vagina ends "blindly" in a pouch. Müllerian regression does not fully complete in approximately one third of all cases, resulting in Müllerian "remnants". Although rare, a few cases of women with CAIS and fully developed Müllerian structures have been reported. In one exceptional case, a 22-year-old with CAIS was found to have a normal cervix, uterus, and fallopian tubes. In an unrelated case, a fully developed uterus was found in a 22-year-old adult with CAIS.

Other subtle differences that have been reported include slightly longer limbs and larger hands and feet due to a proportionally greater stature than unaffected women, larger teeth, minimal or no acne, well developed breasts, and a greater incidence of meibomian gland dysfunction (i.e. dry eye syndromes and light sensitivity).