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.

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.

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.

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.

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.

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.

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.

The procedure to remedy micromastia is breast enlargement, most commonly augmentation mammoplasty using breast implants. Other techniques available involve using muscle flap-based reconstructive surgery techniques (latissimus dorsi and rectus abdominus muscles), microsurgical reconstruction, or fat grafting.

Another potential treatment is hormonal breast enhancement, such as with estrogens.

A number of medications may be used to control symptoms. NSAIDs can be used to reduce painful menstrual periods. Oral contraceptive pills may be prescribed to reduce uterine bleeding and cramps. Anemia may be treated with iron supplementation.

Levonorgestrel intrauterine devices are effective in limiting menstrual blood flow and improving other symptoms. Side effects are typically few as the levonorgestrel (a progestin) is released in low concentration locally. While most levongestrel-IUD studies concentrated on treatment of women without fibroids a few reported good results specifically for women with fibroids including a substantial regression of fibroids.

Cabergoline in a moderate and well-tolerated dose has been shown in two studies to shrink fibroids effectively. The mechanism of action responsible for how cabergoline shrinks fibroids is unclear.

Ulipristal acetate is a synthetic selective progesterone receptor modulator (SPRM) that has tentative evidence to support its use for presurgical treatment of fibroids with low side-effects. Long-term UPA-treated fibroids have shown volume reduction of about 70%. In some cases UPA alone is used to relieve symptoms without surgery.

Danazol is an effective treatment to shrink fibroids and control symptoms. Its use is limited by unpleasant side effects. Mechanism of action is thought to be antiestrogenic effects. Recent experience indicates that safety and side effect profile can be improved by more cautious dosing.

Gonadotropin-releasing hormone analogs cause temporary regression of fibroids by decreasing estrogen levels. Because of the limitations and side effects of this medication, it is rarely recommended other than for preoperative use to shrink the size of the fibroids and uterus before surgery. It is typically used for a maximum of 6 months or less because after longer use they could cause osteoporosis and other typically postmenopausal complications. The main side effects are transient postmenopausal symptoms. In many cases the fibroids will regrow after cessation of treatment, however, significant benefits may persist for much longer in some cases. Several variations are possible, such as GnRH agonists with add-back regimens intended to decrease the adverse effects of estrogen deficiency. Several add-back regimes are possible, tibolone, raloxifene, progestogens alone, estrogen alone, and combined estrogens and progestogens.

Progesterone antagonists such as mifepristone have been tested, there is evidence that it relieves some symptoms and improves quality of life but because of adverse histological changes that have been observed in several trials it can not be currently recommended outside of research setting. Fibroid growth has recurred after antiprogestin treatment was stopped.

Aromatase inhibitors have been used experimentally to reduce fibroids. The effect is believed to be due partially by lowering systemic estrogen levels and partially by inhibiting locally overexpressed aromatase in fibroids. However, fibroid growth has recurred after treatment was stopped. Experience from experimental aromatase inhibitor treatment of endometriosis indicates that aromatase inhibitors might be particularly useful in combination with a progestogenic ovulation inhibitor.

A problem for people with penile agenesis is the absence of a urinary outlet. Before genital metamorphosis, the urethra runs down the anal wall, to be pulled away by the genital tubercle during male development. Without male development this does not occur. The urethra can be surgically redirected to the rim of the anus immediately after birth to enable urination and avoid consequent internal irritation from urea concentrate. In such cases, the perineum may be left devoid of any genitalia, male or female.

A working penis transplant on to an agenetic patient has never been successful. Only one major penis graft was successfully completed. This occurred in China and the patient shortly rejected it on psychological grounds. However a full female or agenetic to male transplant is not yet facilitated to fulfil full reproductive functions.

On March 18, 2013, it was announced that Andrew Wardle, a British man born without a penis, was going to receive a pioneering surgery to create a penis for him. The surgeons hope to "fold a large flap of skin from his arm — complete with its blood vessels and nerves — into a tube to graft onto his pubic area." If the surgery goes well, the odds of starting a family are very good.

Most fibroids do not require treatment unless they are causing symptoms. After menopause fibroids shrink and it is unusual for them to cause problems.

Symptomatic uterine fibroids can be treated by:

- medication to control symptoms

- medication aimed at shrinking tumors

- ultrasound fibroid destruction

- myomectomy or radio frequency ablation

- hysterectomy

- uterine artery embolization

In those who have symptoms uterine artery embolization and surgical options have similar outcomes with respect to satisfaction.

Besides a physical examination, the physician will need imaging techniques to determine the character of the malformation: gynecologic ultrasonography, pelvic MRI, or hysterosalpingography. 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.

In addition, laparoscopy and/or hysteroscopy may be indicated.

In some patients the vaginal development may be affected.

Once RLP has been diagnosed, there are many ways to reduce the pain without jeopardizing the pregnancy.

- Analgesics. Acetaminophen or paracetamol is safe to take during pregnancy, thus is the most commonly prescribed pain reliever for pregnant women with RLP.

- Heat application. Applying a hot compress to the area of pain may give some relief. Hot soaks and hot baths may also help.

- Modifications in movements and position. Triggering factors that can cause RLP are sudden movements, (e.g. sitting up and down, standing up, sneezing, coughing), physical exertion, and long periods in the same resting position. A change in daily activities can help find relief and prevent worsening of the condition. Avoid sudden movements that can cause spasms of the ligament. When about to sneeze or cough, brace yourself by bending and flexing the hips to minimize the pull on the ligaments.

- Rest. Resting is one of the best remedies against RLP. When lying down, changing position slowly and regularly is recommended.

- Physical exercises Daily stretching exercise may be recommended by a gynecologist. An example of such an exercise is kneeling with hands and knees on the floor, then lowering your head to the floor, and keeping your bottom up in the air. The so-called pelvic (hip) tilt exercise also appears to help in reducing pain intensity and duration.

- Surgery. In RLP pathologies involving endometriosis and ademyosis, surgery may be necessary to perform resection of the ligament or removal cysts and myoma.

The first step in management of uterine atony is uterine massage. The next step is pharmacological therapies, the first of which is oxytocin, used because it initiates rhythmic contractions of the uterus, compressing the spiral arteries which should reduce bleeding. The next step in the pharmacological management is the use of methylergometrine, which is an ergot derivative, much like that use in the abortive treatment of migraines. Its side effect of hypertension means its use should not be used in those with hypertension or pre-eclampsia. In those with hypertension, the use of prostaglandin F is indicated (but beware of its use in patients with asthma).

Another option Carbetocin and Carboprost where Oxytocin and ergometrin is inappropriate.

Patients with a double uterus may need special attention during pregnancy as premature birth and malpresentation are common. Cesarean section was performed in 82% of patients reported by Heinonen.

Uterus didelphys, in certain studies, has also been found associated with higher rate of infertility, miscarriage, intrauterine growth retardation, and postpartum bleed.

Congenital anomalies like cryptorchidism, renal agenesis/dysplasia, musculoskeletal and cardiopulmonary anomalies are also common (>50% cases), hence evaluation of the patient for internal anomalies is mandatory.

Although aphallia can occur in any body type, it is considered a substantially more troublesome problem with those who have testes present, and has in the past sometimes been considered justification for assigning and rearing a genetically male infant as a girl. After the theory in the 1950s that gender as a social construct was purely nurture and so an individual child could be raised early on and into one gender or the other regardless of their genetics or brain chemistry. Intersex people generally advocate harshly against coercive genital reassignment however, and encourage infants to be raised choosing their own gender identity. The nurture theory has been largely abandoned and cases of trying to rear children this way have not proven to be successful transitions.

In newborn period or infancy, feminizing operations are recommended for treatment of penile agenesis, but after 2 years, as sexual identification of the patients has appeared, it is advised to perform masculinizing operations in order not to disturb the child psychologically.

Recent advances in surgical phalloplasty techniques have provided additional options for those still interested in pursuing surgery.

Sertoli cell only syndrome is like other non-obstructive azoospermia (NOA) cases are managed by sperm retrieval through testicular sperm extraction (mTESE), micro-surgical testicular sperm extraction (mTESE), or testicular biopsy. On retrieval of viable sperm this could be used in Intracytoplasmic Sperm injection ICSI

In 1979, Levin described germinal cell aplasia with focal spermatogenesis where a variable percentage of seminiferous tubules contain germ cells. It is important to discriminate between both in view of ICSI.

A retrospective analysis performed in 2015 detailed the outcomes of N=148 men with non-obstructive azoospermia and diagnosed Sertoli cell-only syndrome:

- Men with SCOS: 148

- Testicular sperm was successfully retrieved: 35/148

- Successful ICSI: 20/148

- Clinical pregnancy: 4/148

This study considers the effect of FSH levels on clinical success, and it excludes abnormal karyotypes. All patients underwent MD-TESE in Iran. Ethnicity and genetic lineage may have an impact on treatment of azoospermia [citation needed].

A Cochrane review concluded that "simple maternal hydration appears to increase amniotic fluid volume and may be beneficial in the management of oligohydramnios and prevention of oligohydramnios during labour or prior to external cephalic version."

In severe cases oligohydramnios may be treated with amnioinfusion during labor to prevent umbilical cord compression. There is uncertainty about the procedure's safety and efficacy, and it is recommended that it should only be performed in centres specialising in invasive fetal medicine and in the context of a multidisciplinary team.

In case of congenital lower urinary tract obstruction, fetal surgery seems to improve survival, according to a randomized yet small study.

Although rare, this condition is often treatable with surgery. In most cases, the blind hemivagina is opened, and the fluid drained.

At the beginning of the surgery a tourniquet will be applied to the limb. A tourniquet compresses and control the arterial and venous circulation for about 2 hours. The constriction band must be dissected very carefully to avoid damaging the underlying neurovasculature. When the constriction band is excised, there will be a direct closure. This allows the fatty tissue to naturally reposition itself under the skin.

“With complete circumferential constriction bands, it is recommended that a two-stage correction approach be used. At the first operation, one-half of the circumference is excised and the other one-half can be excised after three to six months. This will avoid any problems to the distal circulation in the limb, which may already be compromised. Lymphedema, when present, will significantly improve within a few weeks of the first surgery.”

For the direct closure of the defect after dissecting a constriction band there are two different techniques:

1. Triangular flaps; For this technique the circumference between the two borders must be measured. Depending on the difference the number of triangular flaps can be decided. With a triangular flap you can create more skin.

2. Z/W-plasty; “Z-plasty is a plastic surgery technique that is used to improve the functional and cosmetic appearance of scars. It can elongate a contracted scar or rotate the scar tension line. The middle line of the Z-shaped incision (the central element) is made along the line of greatest tension or contraction, and triangular flaps are raised on opposite sides of the two ends and then transposed.”

In rare cases, if diagnosed in utero, fetal surgery may be considered to save a limb that is in danger of amputation or other deformity. This operation has been successfully performed on fetuses as young as 22 weeks. The Melbourne's Monash Medical Centre in Australia, as well as multiple facilities in the United States of America, have performed successful amniotic band release surgery.

Patients with Leydig cell hypoplasia may be treated with hormone replacement therapy (i.e., with androgens), which will result in normal sexual development and the resolution of most symptoms. In the case of 46,XY (genetically "male") individuals who are phenotypically female and/or identify as the female gender, estrogens should be given instead. Surgical correction of the genitals in 46,XY males may be required, and, if necessary, an orchidopexy (relocation of the undescended testes to the scrotum) may be performed as well.

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".

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

These have been ranked by the UK's National Institute for Health and Clinical Excellence:

- First line

- Intrauterine device with progesterone

- Second Line

- Tranexamic acid an antifibrinolytic agent

- Nonsteroidal anti-inflammatory drugs (NSAIDs).

- Combined oral contraceptive pills to prevent proliferation of the endometrium

- Third line

- Oral progestogen (e.g. norethisterone), to prevent proliferation of the endometrium

- Injected progestogen (e.g. Depo provera)

- Other options

- Gonadotropin-releasing hormone agonist

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.