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.

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.

Risk factors for developing a cystocele are:

- an occupation involving or history of heavy lifting

- pregnancy and childbirth

- chronic lung disease/smoking

- family history of cystocele

- exercising incorrectly

- ethnicity (risk is greater for Hispanic and whites)

- hypoestrogenism

- pelvic floor trauma

- connective tissue disorders

- spina bifida

- hysterectomy

- cancer treatment of pelvic organs* childbirth; correlates to the number of births

- forceps delivery

- age

- chronically high intra-abdominal pressures

- chronic obstructive pulmonary disease

- constipation

- obesity

Connective tissue disorders predispose women to developing cystocele and other pelvic organ prolapse. The tensile strength of the vaginal wall decreases when the structure of the collagen fibers change and become weaker.

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.

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.

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

A cystocele occurs when the muscles, fascia, tendons and connective tissues between a woman’s bladder and vagina weaken, or detach. The type of cystocele that can develop can be due to to three vaginal wall attachment failures. The midline defect, the paravaginal defect, and the transverse defect. The midline defect is a cystocele is caused by the overstretching of the vaginal wall. The paravaginal defect is the separation of the vaginal connective tissue at the arcus tendineus fascia pelvis. The transverse defect is when the pubocervical fascia becomes detached from the top (apex) of the vagina. There is some pelvic prolapse in 40-60% of women who have given birth. Muscle injuries have been identified in women with cystocele. These injuries are more likely to occur in women who have given birth than those who have not. These muscular injuries result in less support to the anterior vaginal wall.

Some women with connective tissue disorders are predisposed to developing anterior vaginal wall collapse. Up to one third of women with Marfan syndrome have a history of vaginal wall collapse. Ehlers-Danlos syndrome in women is associated with a rate of 3 out of 4.

Imperforate hymen is the most common vaginal obstruction of congenital origin. Estimates of the frequency of imperforate hymen vary from 1 in 1000 to 1 in 10,000 females.

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.

The first line of therapy after diagnosis typically involves the administration of the combined oral contraceptive pill, medroxyprogesterone acetate or a gonadotropin-releasing hormone agonist to suppress menstruation and thereby relieve pain. Surgically, cervical agenesis has historically been treated through hysterectomy (removal of the uterus) to relieve symptoms caused by hematocolpos (the accumulation of menstrual fluid in the vagina). Other surgical methods of management involve the creation of an anastomotic connection between the uterus and vagina by neovaginoplasty or recanalization of the cervix. Outcomes in these cases are generally poor, since the natural functions of the cervix—such as mucus production and providing a barrier against ascending infection—cannot be replicated. Furthermore, the success rate of uterovaginal anastomosis is less than 50% and most patients require multiple surgeries while many develop cervical stenotis. Despite this, several pregnancies have been reported in women with cervical agenesis who underwent surgical treatment.

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

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).

A 2008 study found that over 85% of women having a vaginal birth sustain some form of perineal trauma, and 60-70% receive stitches. A retrospective study of 8,603 vaginal deliveries in 1994 found a third degree tear had been clinically diagnosed in only 50 women (0.6%). However, when the same authors used anal endosonography in a consecutive group of 202 deliveries, there was evidence of third degree tears in 35% of first-time mothers and 44% of mothers with previous children. These numbers are confirmed by other researchers in 1999.

A study by the Agency for Healthcare Research and Quality (AHRQ) found that in 2011, first- and second-degree perineal tear was the most common complicating condition for vaginal deliveries in the U.S. among women covered by either private insurance or Medicaid.

Second-degree perineal laceration rates were higher for women covered by private insurance than for women covered by Medicaid.

It is often caused by childbirth (in which case it is known as an obstetric fistula), when a prolonged labor presses the unborn child tightly against the pelvis, cutting off blood flow to the vesicovaginal wall. The affected tissue may necrotize (die), leaving a hole.

Vaginal fistulas can also result from particularly violent cases of rape, especially those involving multiple rapists and/or foreign objects. Some health centers in countries such as the Democratic Republic of Congo have begun to specialize in the surgical repair of vaginal fistulas.

It can also be associated with hysterectomy, cancer operations, radiation therapy and cone biopsy.

Vesicovaginal fistulae are typically repaired either transvaginally or laparoscopically, although patients who have had multiple transvaginal procedures sometimes attempt a final repair through a large abdominal incision, or laparotomy.

The laparoscopic (minimally invasive) approach to VVF repair has become more prevalent due to its greater visualization, higher success rate, and lower rate of complications.

An imperforate hymen is formed during fetal development when the sinovaginal bulbs fail to canalize with the rest of the vagina. Although some instances of familial occurrence have been reported, the condition's occurrence is mostly sporadic, and no genetic markers or mutations have been linked to its cause.

Rectoceles result from the weakening of the pelvic floor also called pelvic organ prolapse. Weakened pelvic structures occur as a result of an episiotomy during previous births, even decades later. Other causes of pelvic floor prolapse can be advanced age, multiple vaginal deliveries, and birthing trauma. Birthing trauma includes vacuum delivery, forceps delivery, and perineal tear. In addition, a history of chronic constipation and excessive straining with bowel movements are thought to play a role in rectocele. Multiple gynecological or rectal surgeries can also lead to weakening of the pelvic floor. Births that involve babies over nine pounds in weight, or rapid births can contribute to the development of rectocele.

A hysterectomy or other pelvic surgery can be a cause, as can chronic constipation and straining to pass bowel movements. It is more common in older women than in younger ones; estrogen which helps to keep the pelvic tissues elastic decreases after menopause.

Hematometra develops when the uterus becomes distended with blood secondary to obstruction or atresia of the lower reproductive tract—the uterus, cervix or vagina—which would otherwise provide an outflow for menstrual blood. It is most commonly caused by congenital abnormalities, including imperforate hymen, transverse vaginal septum or vaginal hypoplasia. Other causes are acquired, such as cervical stenosis, intrauterine adhesions, endometrial cancer, and cervical cancer.

Additionally, hematometra may develop as a complication of uterine or cervical surgery such as endometrial ablation, where scar tissue in the endometrium can "wall off" sections of endometrial glands and stroma causing blood to accumulate in the uterine cavity. It can also develop after abortion, as well as after childbirth. It can also develop after female genital mutilation.

Treatment depends on the severity of the problem, and may include non-surgical methods such as changes in diet (increase in fiber and water intake), pelvic floor exercises such as Kegel exercises, use of stool softeners, hormone replacement therapy for post-menopausal women and insertion of a pessary into the vagina. A high fiber diet, consisting of 25-30 grams of fiber daily, as well as increased water intake (typically 6-8 glasses daily), help to avoid constipation and straining with bowel movements, and can relieve symptoms of rectocele.

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.

Several techniques are used to reduce the risk of tearing, but with little evidence for efficacy. Antenatal digital perineal massage is often advocated, and may reduce the risk of trauma only in nulliparous women. ‘Hands on’ techniques employed by midwives, in which the foetal head is guided through the vagina at a controlled rate have been widely advocated, but their efficacy is unclear. Waterbirth and labouring in water are popular for several reasons, and it has been suggested that by softening the perineum they might reduce the rate of tearing. However, this effect has never been clearly demonstrated.

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.

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.

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.