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.

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 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.

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.

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.

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

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.

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.

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).

Hematometra typically presents as cyclic, cramping pain in the midline of the pelvis or lower abdomen. Patients may also report urinary frequency and urinary retention. Premenopausal women with hematometra often experience abnormal vaginal bleeding, including dysmenorrhea (pain during menstruation) or amenorrhea (lack of menstruation), while postmenopausal women are more likely to be asymptomatic. Due to the accumulation of blood in the uterus, patients may develop low blood pressure or a vasovagal response. When palpated, the uterus will typically feel firm and enlarged.

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.

The symptoms of a cystocele may include:

- a vaginal bulge

- the feeling that something is falling out of the vagina

- the sensation of pelvic heaviness or fullness

- difficulty starting a urine stream

- a feeling of incomplete urination

- frequent or urgent urination

- fecal incontinence

- frequent urinary tract infections

A bladder that has dropped from its normal position and into the vagina can cause some forms of incontinence and incomplete emptying of the bladder.

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.

Uterine hypoplasia, also known as naive uterus or infantile uterus, is a reproductive disorder characterized by hypoplasia of the uterus. It is usually due to pubertal failure/hypogonadism and may be treated with puberty induction using estrogens and/or progestogens.

Vesicovaginal fistula, or VVF, is an abnormal fistulous tract extending between the bladder (or vesico) and the vagina that allows the continuous involuntary discharge of urine into the vaginal vault.

In addition to the medical sequela from these fistulas, they often have a profound effect on the patient's emotional well-being.

Complications may include urinary retention, recurring urinary tract infections and incontinence. The anterior vaginal wall may actually protrude though the vaginal introitus (opening). This can interfere with sexual activity. Recurrent urinary tract infections are common for those who have urinary retention. In addition, though cystocele can be treated, some treatments may not alleviate troubling symptoms, and further treatment may need to be performed. Cystocele may effect the quality of life. Women who have cystocele tend to avoid leaving their home and social situations. The resulting incontinence puts women at risk of being placed in a nursing home or long term care facility.

Vesicovaginal fistula (VVF) is a subtype of female urogenital fistula (UGF).

A vaginal obstruction is often caused by an imperforate hymen or, less commonly, a transverse vaginal septum. A sign of vaginal obstruction is hydrocolpos, that is, accumulation of watery fluid within the vagina. It may extend to become "hydrometrocolpos", that is, accumulation of watery fluid within the vagina as well as within the uterus.

Mild cases may simply produce a sense of pressure or protrusion within the vagina, and the occasional feeling that the rectum has not been completely emptied after a bowel movement. Moderate cases may involve difficulty passing stool (because the attempt to evacuate pushes the stool into the rectocele instead of out through the anus), discomfort or pain during evacuation or intercourse, constipation, and a general sensation that something is "falling down" or "falling out" within the pelvis. Severe cases may cause vaginal bleeding, intermittent fecal incontinence, or even the prolapse of the bulge through the mouth of the vagina, or rectal prolapse through the anus. Digital evacuation, or, manual pushing, on the posterior wall of the vagina helps to aid in bowel movement in a majority of cases of rectocele. Rectocele can be a cause of symptoms of obstructed defecation.

Genital symptoms include dryness, itching, burning, soreness, pressure, white discharge, malodorous discharge due to infection, painful sexual intercourse, bleeding after intercourse. In addition, sores and cracks may occur spontaneously. Atrophic vaginitis is one possible cause of postmenopausal bleeding (PMB).

Urinary symptoms include painful urination, blood in the urine, increased frequency of urination, incontinence, and increased likelihood and occurrence of infections.

Hydrocolpos is the distension of the vagina caused by accumulation of fluid due to congenital vaginal obstruction. The obstruction is often caused by an imperforate hymen or less commonly a transverse vaginal septum. The fluid consists of cervical and endometrial mucus or in rare instances urine accumulated through a vesicovaginal fistula proximal to the obstruction. In some cases it is associated with Bardet-Biedl Syndrome. If it occurs in prepubertal girls, it may show up as abdominal swelling. It may be detected by using ultrasound. It may also present at birth as a distended lower abdomen and vagina. It also associated with vaginal atresia.

A Gartner's duct cyst (sometimes incorrectly referred to as "vaginal inclusion cyst") is a benign vaginal cystic lesion that arises from the Gartner's duct, which is a vestigial remnant of the mesonephric duct (wolffian duct) in females. They are typically small asymptomatic cysts that occur along the lateral walls of the vagina, following the course of the duct. They can present in adolescence with painful menstruation (Dysmenorrhea) or difficulty inserting a tampon. They can also enlarge to substantial proportions and be mistaken for urethral diverticulum or other structures.

There is a small association between Gartner's duct cysts and metanephric urinary anomalies, such as ectopic ureter & ipsilateral renal hypoplasia. Because of this, imaging is recommended before excision.

Atrophic vaginitis (also known as vaginal atrophy, vulvovaginal atrophy, or urogenital atrophy) is an inflammation of the vagina (and the outer urinary tract) due to the thinning and shrinking of the tissues, as well as decreased lubrication. These symptoms are due to a lack of the reproductive hormone estrogen.

The most common cause of vaginal atrophy is the decrease in estrogen which happens naturally during perimenopause, and increasingly so in post-menopause. However this condition can occur in other circumstances that result in decreased estrogen such as breastfeeding and the use of medications intended to decrease estrogen too, for example, treat endometriosis.

The symptoms can include vaginal soreness and itching, as well as painful intercourse, and bleeding after sexual intercourse. The shrinkage of the tissues and loss of flexibility can be extreme enough to make intercourse impossible.