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.

In order to facilitate sexual intercourse, the main treatments are self-dilation methods (using intra-vaginal cylinders of increasing size) and surgical vaginoplasty to lengthen the vagina.

Self-dilation has a high success rate, estimated at 75%, and is usually the first-line treatment due to low surgical invasiveness. Overall, the complication rates are significantly lower with dilation than with vaginoplasty.

Surgery is indicated when there is inability or reluctance to perform self-dilation, or where it is performed but with failed result. One appropriate surgical variant is the "Vecchietti technique". In this procedure, an olive-shaped pressure device is pressed towards the potential vaginal space by a thread that goes through the skin, behind the urinary bladder and pubic bone and exits the skin in the hypogastrium, where it is attached to a plate that provides counter-traction. Vaginoplasty can also be performed using a skin graft or an intestinal graft. Traction vaginoplasty such as the "Vecchietti technique" seems to have the highest success rates both anatomically (99%) and functionally (96%), whereas skin graft procedures and intestinal procedures have the lowest successful outcomes (83–95%).

After vaginoplasty, available evidence suggests that continued self-dilation is needed to maintain patency in periods of coital inactivity.

There are several methods of treatment for individuals with vaginal atresia. The first method of treatment that is recommended would be self-dilation of the vagina. A doctor may first recommend that the patient first attempts to create a vagina themselves through the process self-dilation. The self dilation technique consists of using vaginal dilators, which are small round tubes that vary in size and are similar in size and shape to tampons. Vaginal dilators may be pressed alongside the vaginal area on a regular basis in order to further open the vaginal canal. Frank's procedure is a technique that used a progressive series of vaginal dilators that are inserted into the dimple of the vagina while using pressure. This will widen any space that exists between the bladder and the rectum. Frank's procedure can be performed directly by the patient, therefore requiring no surgery or anesthesia. The procedure/technique can take months to complete, with regular compliance necessary. The overall success rate for females who use Frank's procedure is 80%. If this procedure does not work, then surgery would be the next method of treatment. Another alternative form of treatment would be surgery, or the creation of a new vagina.

There is no cure available for individuals with Bardet-Biedl Syndrome, however there are methods of treatment for some of the signs and symptoms within each individual. Corrective surgery of malformation related to the disorder may be an option for treatment. Genetic counseling is also something that could be beneficial to families with this disorder.

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.

Surgical intervention depends on the extent of the individual problem. With a didelphic uterus surgery is not usually recommended.

A uterine septum can be resected in a simple out-patient procedure that combines laparoscopy and hysteroscopy. This procedure greatly decreases the rate of miscarriage for women with this anomaly.

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.

A number of treatments have become available to create a functioning vagina, yet in the absence of a uterus currently no surgery is available to make pregnancy possible. Standard approaches use vaginal dilators and/or surgery to develop a functioning vagina to allow for penetrative sexual intercourse. A number of surgical approaches have been used. In the McIndoe procedure, a skin graft is applied to form an artificial vagina. After the surgery, dilators are still necessary to prevent vaginal stenosis. The Vecchietti procedure has been shown to result in a vagina that is comparable to a normal vagina in patients. In the Vecchietti procedure, a small plastic “olive” is threaded against the vaginal area, and the threads are drawn through the vaginal skin, up through the abdomen and through the navel using laparoscopic surgery. There the threads are attached to a traction device. The operation takes about 45 minutes. The traction device is then tightened daily so the olive is pulled inwards and stretches the vagina by approximately 1 cm per day, creating a vagina approximately 7 cm deep in 7 days, although it can be more than this. Another approach is the use of an autotransplant of a resected sigmoid colon using laparoscopic surgery; results are reported to be very good with the transplant becoming a functional vagina.

Uterine transplantation has been performed in a number of people with MRKH, but the surgery is still in the experimental stage. Since ovaries are present, people with this condition can have genetic children through IVF with embryo transfer to a gestational carrier. Some also choose to adopt. In October 2014 it was reported that a month earlier a 36-year-old Swedish woman became the first person with a transplanted uterus to give birth to a healthy baby. She was born without a uterus, but had functioning ovaries. She and the father went through IVF to produce 11 embryos, which were then frozen. Doctors at the University of Gothenburg then performed the uterus transplant, the donor being a 61-year-old family friend. One of the frozen embryos was implanted a year after the transplant, and the baby boy was born prematurely at 31 weeks after the mother developed pre-eclampsia.

Promising research include the use of laboratory-grown structures, which are less subject to the complications of non-vaginal tissue, and may be grown using the person's own cells as a culture source. The recent development of engineered vaginas using the patient's own cells has resulted in fully functioning vaginas capable of menstruation and orgasm in a number of patients showing promise of fully correcting this condition in some of the sufferers.

Before surgical intervention in adolescents, symptoms can be relieved by the combined oral contraceptive pill taken continuously to suppress the menstrual cycle or NSAIDs to relieve pain. Surgical treatment of the imperforate hymen by hymenotomy typically involves making cruciate incisions in the hymen, excising segments of hymen from their bases, and draining the vaginal canal and uterus. For affected girls who wish (or whose parents wish) to have their hymens preserved, surgical techniques to excise of a central flange of the hymen can be used. The timing of surgical hymen repair is controversial: some doctors believe it is best to intervene immediately after the neonatal period, while others believe that surgical repair should be delayed until puberty, when estrogenization is complete.

Cystocele may be mild enough not to result in symptoms that are troubling to a woman. In this case, steps to prevent it from getting worse.These are:

- smoking cessation

- losing weight

- pelvic floor strengthening

- treatment of a chronic cough

- maintaining healthy bowel habits

- eating high fiber foods

- avoiding constipation and straining

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%).

Surgery (orchiopexy) to retrieve the testes and position them in the scrotum is the primary treatment. Occasionally they are unsalvageable if located high in the retroperitoneum. During this surgery, the uterus is usually removed and attempts made to dissect away Müllerian tissue from the vas deferens and epididymis to improve the chance of fertility. If the person has male gender identity himself and the testes cannot be retrieved, testosterone replacement will be usually necessary at puberty should the affected individual choose to pursue medical attention. Lately, laparoscopic hysterectomy is offered to patients as a solution to both improve the chances of fertility and to prevent the occurrences of neoplastic tissue formation.

A simple cruciate incision followed by excision of tags of hymen allows drainage of the retained menstrual blood. A thicker transverse vaginal septum can be treated with Z-plasty. A blind vagina will require a partial or complete vaginoplasty. Hematosalpinx may require laprotomy or laparoscopy for removal and reconstruction of affected tube.

Infertility may require assisted reproductive techniques.

A septum can be resected with surgery. Hysteroscopic removal of a uterine septum is generally the preferred method, as the intervention is relatively minor and safe in experienced hands. A follow-up imaging study should demonstrate the removal of the septum.

Tactile cold scissor metroplasty was described as a back technique for hysteroscopic challenges that interfere with proper visualization or uterine distention

It is not considered necessary to remove a septum that has not caused problems, especially in women who are not considering pregnancy. There is controversy over whether a septum should be removed prophylactically to reduce the risk of pregnancy loss prior to a pregnancy or infertility treatment.

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.

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.

It is generally treated surgically, with a hymenotomy or other surgery to remove any tissue that blocks the menstrual flow.

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).

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.

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

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.

Treatment options range from no treatment for a mild cystocele to surgery for a more extensive cystocele. If a cystocele is not bothersome, the clinician may only recommend avoiding heavy lifting or straining that could cause the cystocele to worsen. If symptoms are moderately bothersome, the doctor may recommend a pessary, a device placed in the vagina to hold the bladder in place. Treatment can consist of a combination of non-surgical and surgical management. Treatment choice is also related to age, desire to have children, severity of impairment, desire to continue sexual intercourse and other diseases that a woman may have.

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.

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.

Some have hypothesized that supraphysiological levels of estrogen may reduce the diminished bone mineral density associated with CAIS. Data has been published that suggests affected women who were not compliant with estrogen replacement therapy, or who had a lapse in estrogen replacement, experienced a more significant loss of bone mineral density. Progestin replacement therapy is seldom initiated, due to the absence of a uterus. Androgen replacement has been reported to increase a sense of well-being in gonadectomized women with CAIS, although the mechanism by which this benefit is achieved is not well understood.