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.

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.

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.

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

Patients with cervical agenesis typically present in early adolescence, around the time of menarche, with amenorrhea and cyclic pelvic pain caused by the obstruction of menstrual flow from the uterus.

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.

Affected newborns may present with acute urinary retention. In adolescent females, the most common symptoms of an imperforate hymen are cyclic pelvic pain and amenorrhea; other symptoms associated with hematocolpos include urinary retention, constipation, back pain, nausea, and diarrhea.

A longitudinal vaginal septum develops during embryogenesis when there is an incomplete fusion of the lower parts of the two Müllerian ducts. As a result, there is a "double vagina". There may be associated duplications of the more cranial parts of the Müllerian derivatives, a double cervix, and either a uterine septum or uterus didelphys (double uterus).

The person with a longitudinal vaginal septum may be asymptomatic and not aware of the condition. If dyspareunia is a problem a simple resection of the septum could be performed.

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.

Vaginal hypoplasia is the underdevelopment or incomplete development of the vagina. Vaginal hypoplasia can vary in severity from being smaller than normal to being completely absent. The absence of a vagina is a result of vaginal agenesis. Diagnostically, it may look similar to a vaginal obstruction. 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.

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.

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

Eugonadotropic primary amenorrhea and cyclical lower abdominal pain are the chief presenting complaints of hematocolpos. Patient may be brought in emergency urinary retention.

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.

Cryptomenorrhea or cryptomenorrhoea, also known as hematocolpos, is a condition where menstruation occurs but is not visible due to an obstruction of the outflow tract. Specifically the endometrium is shed, but a congenital obstruction such as a vaginal septum or on part of the hymen retains the menstrual flow. A patient with cryptomenorrhea will appear to have amenorrhea but will experience cyclic menstrual pain. The condition is surgically correctable.

The patient usually presents at the age of puberty when the commencement of menstruation blood gets collected in the vagina and gives rise to symptoms.

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.

Where a urethrocele causes difficulty in urinating, this can lead to cystitis.

As the vagina is largely derived from the Müllerian ducts, lack of fusion of the two ducts can lead to the formation of a vaginal duplication and lack of absorption of the wall between the two ducts will leave a residual septum, leading to a "double vagina". This condition may be associated with a uterus didelphys or a uterine septum. Since the condition is internal and usually asymptomatic, a person may not be aware of having a "double vagina." If necessary, the partition can be surgically corrected, however, there is no valid medical reason for such a procedure.

The presence of unusual lumps in the wall or base of the vagina is always abnormal. The most common of these is Bartholin's cyst. The cyst, which can feel like a pea, is formed by a blockage in glands which normally supply the opening of the vagina. This condition is easily treated with minor surgery or silver nitrate. Other less common causes of small lumps or vesicles are herpes simplex. They are usually multiple and very painful with a clear fluid leaving a crust. They may be associated with generalized swelling and are very tender. Lumps associated with cancer of the vaginal wall are very rare and the average age of onset is seventy years. The most common form is squamous cell carcinoma, then cancer of the glands or adenocarcinoma and finally, and even more rarely, melanoma.

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).

There are often no symptoms associated with a urethrocele. When present, symptoms include stress incontinence, increased urinary frequency, and urinary retention (difficulty in emptying the bladder). Pain during sexual intercourse may also occur.

An imperforate hymen is a congenital disorder where a hymen without an opening completely obstructs the vagina. It is caused by a failure of the hymen to perforate during fetal development. It is most often diagnosed in adolescent girls when menstrual blood accumulates in the vagina and sometimes also in the uterus. It is treated by surgical incision of the hymen.

Hematocolpos is a medical condition in which the vagina fills with menstrual blood. It is often caused by the combination of menstruation with an imperforate hymen. It is sometimes seen in Robinow syndrome, uterus didelphys, or other congenital conditions.

A related disorder is hematometra, where the uterus fills with menstrual blood. It presents after puberty as primary amenorrhoea, recurrent pelvic pain with a pelvic mass. This can be caused by a congenital stenosis of the cervix, or by a complication of a surgical treatment.

A Suprapubc bulge is caused by hematocolpos. Vaginal introitus shows a blue bulging membrane.

Uterus didelphys (sometimes also "uterus didelphis") represents a uterine malformation where the uterus is present as a paired organ when the embryogenetic fusion of the Müllerian ducts fails to occur. As a result, there is a double uterus with two separate cervices, and rarely a double vagina as well. Each uterus has a single horn linked to the ipsilateral fallopian tube that faces its ovary.

In non human species ("e.g." nematodes), a didelphic genital tract may be normal rather than a malformation. Such species are described as didelphic, as opposed to monodelphic, with a single tract.