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.

Although there is no cure for 13q deletion syndrome, symptoms can be managed, usually with the involvement of a neurologist, rehabilitation physician, occupational therapist, physiotherapist, psychotherapist, nutritionist, special education professional, and/or speech therapist. If the affected child's growth is particularly slow, growth hormone treatment can be used to augment growth. Plastic surgeries can repair cleft palates, and surgical repair or monitoring by a pediatric cardiologist can manage cardiac defects. Some skeletal, neurological, genitourinary, gastrointestinal, and ophthalmic abnormalities can be definitively treated with surgery. Endocrine abnormalities can often be managed medically. Special educators, speech and occupational therapists, and physiotherapists can help a child develop skills in and out of school.

While there is no specific treatment for the underlying genetic cause of LFS; corrective procedures, preventive intervention measures and therapies may be considered in the treatment and management of the many craniofacial, orthopedic and psychiatric problems associated with the disorder. More pressing issues such as cardiac involvement or epileptic seizures should be routinely examined and monitored. Close attention and specialized follow-up care, including neuropshycological evaluation methods and therapies, and special education, should be given to diagnose and prevent psychiatric disorders and related behavioral problems such as psychosis and outbursts of aggression.

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.

Imperforate anus usually requires immediate surgery to open a passage for feces unless a fistula can be relied on until corrective surgery takes place. Depending on the severity of the imperforate, it is treated either with a perineal anoplasty or with a colostomy.

While many surgical techniques to definitively repair anorectal malformations have been described. The posterior sagittal approach (PSARP) has become the most popular. It involves dissection of the perineum without entry into the abdomen and 90% of defects in boys can be repaired this way.

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.

With a high lesion, many children have problems controlling bowel function and most also become constipated. With a low lesion, children generally have good bowel control, but they may still become constipated.

For children who have a poor outcome for continence and constipation from the initial surgery, further surgery to better establish the angle between the anus and the rectum may improve continence and, for those with a large rectum, surgery to remove that dilated segment may significantly improve the bowel control for the patient. An antegrade enema mechanism can be established by joining the appendix to the skin (Malone stoma); however, establishing more normal anatomy is the priority.

Since the symptoms caused by this disease are present at birth, there is no “cure.” The best cure that scientists are researching is awareness and genetic testing to determine risk factors and increase knowledgeable family planning. Prevention is the only option at this point in time for a cure.

While there is no cure for JBS, treatment and management of specific symptoms and features of the disorder are applied and can often be successful. Variability in the severity of JBS on a case-by-case basis determines the requirements and effectiveness of any treatment selected.

Pancreatic insufficiency and malabsorption can be managed with pancreatic enzyme replacement therapy, such as pancrelipase supplementation and other related methods.

Craniofacial and skeletal deformities may require surgical correction, using techniques including bone grafts and osteotomy procedures. Sensorineural hearing loss can be managed with the use of hearing aids and educational services designated for the hearing impaired.

Special education, specialized counseling methods and occupational therapy designed for those with mental retardation have proven to be effective, for both the patient and their families. This, too, is carefully considered for JBS patients.

Treatments for the condition vary depending on its severity. The most immediate and effective treatment in the majority of cases is a surgical repair to close the fistula/s and reconnect the two ends of the esophagus to each other. Although this is usually done through an incision between the ribs on right side of the baby, a technique using three small incisions (thoracoscopy) is being used at some centers. In a minority of cases, the gap between upper and lower esophageal segments may be too long to bridge. In some of these so-called long gap cases, though, an advanced surgical treatment developed by John Foker, MD, may be utilized to elongate and then join together the short esophageal segments. Using the Foker technique, surgeons place traction sutures in the tiny esophageal ends and increase the tension on these sutures daily until the ends are close enough to be sewn together. The result is a normally functioning esophagus, virtually indistinguishable from one congenitally well formed. Unfortunately, the results have been somewhat difficult to replicate by other surgeons and the need for multiple operations has tempered enthusiasm for this approach.

The optimal treatment in cases of long gap esophageal atresia remains controversial. Traditional surgical approaches include gastrostomy followed by gastric pull-up, colonic transposition and jejunum transposition. Gastric pull-up has been the preferred approach at many specialized centers, including Great Ormond Street (London) and Mott Children's Hospital (Ann Arbor). Gastrostomy, or G-tube, allows for tube feedings into the stomach through the abdominal wall. Often a cervical esophagostomy will also be done, to allow the saliva which is swallowed to drain out a hole in the neck. Months or years later, the esophagus may be repaired, sometimes by using a segment of bowel brought up into the chest, interposing between the upper and lower segments of esophagus.

Post operative complications sometimes arise, including a leak at the site of closure of the esophagus. Sometimes a stricture, or tight spot, will develop in the esophagus, making it difficult to swallow. This can usually be dilated using medical instruments. In later life, most children with this disorder will have some trouble with either swallowing or heartburn or both. Esophageal dismotility occurs in 75-100% of patients.

Tracheomalacia—a softening of the trachea, usually above the carina (carina of trachea), but sometimes extensive in the lower bronchial tree as well—is another possible serious complication. Even after esophageal repair (anastomosis) the relative flaccidity of former proximal pouch (blind pouch, above) along with esophageal dysmotility can cause fluid buildup during feeding. Owing to proximity, pouch ballooning can cause tracheal occlusion. Severe hypoxia ("dying spells") follows and medical intervention can often be required.

A variety of treatments for tracheomalacia associated with esophageal atresia are available. If not severe, the condition can be managed expectantly since the trachea will usually stiffen as the infant matures into the first year of life. When only the trachea above the carina is compromised, one of the "simplest" interventions is aortopexy wherein the aortic loop is attached to the rear of the sternum, thereby mechanically relieving pressure from the softened trachea. An even simpler intervention is stenting. However, epithelial cell proliferation and potential incorporation of the stent into the trachea can make subsequent removal dangerous.

Colostomy is recommended by most surgeons, and has a good prognosis, with 90% of patients regaining normal bowel control. Since the rectal opening and anal orifice in a vestibular fistula tend to be short and narrow, a colostomy is usually performed to allow decompression of the bowel unless the orifice is wide enough to allow normal defecation. Colostomy is often followed by posterior sagittal anorectoplasty (PSARP), a surgical procedure to repair the anal orifice, at a later date. Some surgeons prefer to perform an immediate PSARP without a colostomy first, while others perform neither a colostomy nor a PSARP and instead opt for a simple dilatation of the orifice to allow stool to pass and the bowel to decompress. It has been suggested that only experienced surgeons should perform repair without an initial colostomy.

The only potentially curative treatment for complete rectal prolapse is surgery, however in those patients with medical problems that make them unfit for surgery, and those patients who have minimal symptoms, conservative measures may benefit. Dietary adjustments, including increasing dietary fiber may be beneficial to reduce constipation, and thereby reduce straining. A bulk forming agent (e.g. psyllium) or stool softener can also reduce constipation.

The prognostic outcomes for this type of cloaca are good for bowel control and urinary function. The surgical repair for this type of cloaca can usually be done by performing posterior sagittal approach without opening of the abdomen. A common channel longer than 3 cm in length usually has poor sphincter muscles and a poor sacrum, suggesting a prognostic outcome for bowel control and urinary function to be less likely. Common channels longer than 3 cm are generally considered more complex and more technically challenging in surgical repair.

Hormonal suppressive therapy with luteinizing hormone receptor agonists like leuprolide can be used to treat the seizure component, and are effective in most patients.

Surgery is offered if there is failure of medical therapy or rapid growth of lesion, with specific options including stereotactic thermocoagulation, gamma knife radiosurgery, and physical resection by transsphenoidal microsurgery. Surgical response is typically better when the seizure focus has been found by EEG to originate in or near the mass. The specific location of the lesion relative to the pituitary and infundibulum and the amount of hormonal disturbance at presentation can help predict risk of hypopituitarism following surgery.

PELVIS syndrome is a congenital condition characterized by perineal hemangioma, external genitalia malformations, lipomyelomeningocele, vesicorenal abnormalities, imperforate anus, and skin tag.

There are several stages to treating an anal fistula:

Definitive treatment of a fistula aims to stop it recurring. Treatment depends on where the fistula lies, and which parts of the internal and external anal sphincters it crosses.

There are several options:

- Doing nothing — a drainage seton can be left in place long-term to prevent problems. This is the safest option although it does not definitively cure the fistula.

- Lay-open of fistula-in-ano — this option involves an operation to cut the fistula open. Once the fistula has been laid open it will be packed on a daily basis for a short period of time to ensure that the wound heals from the inside out. This option leaves behind a scar, and depending on the position of the fistula in relation to the sphincter muscle, can cause problems with incontinence. This option is not suitable for fistulae that cross the entire internal and external anal sphincter.

- Cutting seton — if the fistula is in a high position and it passes through a significant portion of the sphincter muscle, a cutting seton (from the Latin "seta", "bristle") may be used. This involves inserting a thin tube through the fistula tract and tying the ends together outside of the body. The seton is tightened over time, gradually cutting through the sphincter muscle and healing as it goes. This option minimizes scarring but can cause incontinence in a small number of cases, mainly of flatus. Once the fistula tract is in a low enough position it may be laid open to speed up the process, or the seton can remain in place until the fistula is completely cured. This was the traditional modality used by physicians in Ancient Egypt and formally codified by Hippocrates, who used horsehair and linen.

- Seton stitch — a length of suture material looped through the fistula which keeps it open and allows pus to drain out. In this situation, the seton is referred to as a draining seton. The stitch is placed close to the ano-rectal ring – which encourages healing and makes further surgery easy.

- Fistulotomy — till anorectal ring

- Colostomy — to allow healing

- Fibrin glue injection is a method explored in recent years, with variable success. It involves injecting the fistula with a biodegradable glue which should, in theory, close the fistula from the inside out, and let it heal naturally. This method is perhaps best tried before all others since, if successful, it avoids the risk of incontinence, and creates minimal stress for the patient.

- Fistula plug involves plugging the fistula with a device made from small intestinal submucosa. The fistula plug is positioned from the inside of the anus with suture. According to some sources, the success rate with this method is as high as 80%. As opposed to the staged operations, which may require multiple hospitalizations, the fistula plug procedure requires hospitalization for only about 24 hours. Currently, there are two different anal fistula plugs cleared by the FDA for treating ano-rectal fistulae in the United States. This treatment option does not carry any risk of bowel incontinence. In the systematic review published by Dr Pankaj Garg, the success rate of the fistula plug is 65-75%.

- Endorectal advancement flap is a procedure in which the internal opening of the fistula is identified and a flap of mucosal tissue is cut around the opening. The flap is lifted to expose the fistula, which is then cleaned and the internal opening is sewn shut. After cutting the end of the flap on which the internal opening was, the flap is pulled down over the sewn internal opening and sutured in place. The external opening is cleaned and sutured. Success rates are variable and high recurrence rates are directly related to previous attempts to correct the fistula.

- LIFT Technique is a novel modified approach through the intersphincteric plane for the treatment of fistula-in-ano, known as LIFT (ligation of intersphincteric fistula tract) procedure. LIFT procedure is based on secure closure of the internal opening and removal of infected cryptoglandular tissue through the intersphincteric approach. Essential steps of the procedure include, incision at the intersphincteric groove, identification of the intersphincteric tract, ligation of intersphincteric tract close to the internal opening and removal of intersphincteric tract, scraping out all granulation tissue in the rest of the fistulous tract, and suturing of the defect at the external sphincter muscle. The procedure was developed by Thai colorectal surgeon, Arun Rojanasakul, The first reports of preliminary healing result from the procedure were 94% in 2007. Additional ligation of the intersphincteric fistula tract did not improve the outcome after endorectal advancement flap.

- Fistula clip closure (OTSC Proctology) is the latest surgical development, which involves the closure of the internal fistula opening with a superelastic clip made of nitinol (OTSC). During surgery, the fistula tract is debrided with a special fistula brush and the clip is transanally applied with the aid of a preloaded clip applicator. The surgical principle of this technique relies on the dynamic compression and permanent closure of the internal fistula opening by the superelastic clip. Consequently, the fistula tract dries out and heals instead of being kept open by continuous feeding with stool and fecal organisms. This minimally-invasive sphincter-preserving technique has been developed and clinically implemented by the German surgeon Ruediger Prosst. First clinical data of the clip closure technique demonstrate a success rate of 90% for previously untreated fistulae and a success rate of 70% for recurrent fistulae.

- PERFACT Procedure is another latest addition to the armamentarium to treat complex and highly complex fistula-in-ano. It is a minimally cutting procedure as both the anal sphincters (internal and external sphincters) are not cut/damaged at all. Therefore, the risk of incontinence is minimal. PERFACT procedure (proximal superficial cauterization, emptying regularly fistula tracts and curettage of tracts) entails two steps: superficial cauterization of mucosa at and around the internal opening and keeping all the tracts clean. The principle is to permanently close the internal opening by granulation tissue. This is achieved by superficial electrocauterization at and around the internal opening and subsequently allowing the wound to heal by secondary intention. Early results of this procedure are quite encouraging for complex fistula-in-ano (86.4% in highly complex anal fistulae). The procedure is effective even in fistula associated with abscess, supralevator fistula-in-ano and fistula where the internal opening is non-localizable.

Because the variability of this disease is so great and the way that it reveals itself could be multi-faceted; once diagnosed, a multidisciplinary team is recommended to treat the disease and should include a craniofacial surgeon, ophthalmologist, pediatrician, pediatric urologist, cardiologist, pulmonologist, speech pathologist, and a medical geneticist. Several important steps must be followed, as well.

- Past medical history

- Physical examination with special attention to size and measurements of facial features, palate, heart, genitourinary system and lower respiratory system

- Eye evaluation

- Hypospadias assessment by urologist

- Laryngoscopy and chest x-ray for difficulties with breathing/swallowing

- Cleft lip/palate assessment by craniofacial surgeon

- Assessment of standard age developmental and intellectual abilities

- Anal position assessment

- Echocardiogram

- Cranial imaging

Many surgical repairs may be needed, as assessed by professionals. Furthermore, special education therapies and psychoemotional therapies may be required, as well. In some cases, antireflux drugs can be prescribed until risk of breathing and swallowing disorders are removed. Genetic counseling is highly advised to help explain who else in the family may be at risk for the disease and to help guide family planning decisions in the future.

Because of its wide variability in which defects will occur, there is no known mortality rate specifically for the disease. However, the leading cause of death for people with Opitz G/BBB syndrome is due to infant death caused by aspiration due to esophageal, pharyngeal or laryngeal defects.

Fortunately, to date there are no factors that can increase the expression of symptoms of this disease. All abnormalities and symptoms are present at birth.

Some people will have an active infection when they present with a fistula, and this requires clearing up before definitive treatment can be decided.

Antibiotics can be used as with other infections, but the best way of healing infection is to prevent the buildup of pus in the fistula, which leads to abscess formation. This can be done with a seton.

After diagnosing rectovaginal fistula, it is best to wait for around 3 months to allow the inflammation to subside. For low fistulae, a vaginal approach is best, while an abdominal repair would be necessary for a high fistula at the posterior fornix.

A circular incision is made around the fistula and vagina is separated from the underlying rectum with a sharp circumferential dissection. The entire fistulous tract, along with a small rim of rectal mucosa is incised. The rectal wall is then closed extramucosally.

Most rectovaginal fistuals will need surgery to fix. Medications such as antibiotics and Infliximab might be prescribed to help close the rectovaginal fistula or prepare for surgery.

Affected individuals have a somewhat shortened lifespan. The maximum described lifespan is 67 years. Adults with 13q deletion syndrome often need support services to maintain their activities of daily living, including adult day care services or housing services.

Initial steps to alleviate anismus include dietary adjustments and simple adjustments when attempting to defecate. Supplementation with a bulking agent such as psyllium 3500 mg per day will make stool more bulky, which decreases the effort required to evacuate. Similarly, exercise and adequate hydration may help to optimise stool form. The anorectal angle has been shown to flatten out when in a squatting position, and is thus recommended for patients with functional outlet obstruction like anismus. If the patient is unable to assume a squatting postures due to mobility issues, a low stool can be used to raise the feet when sitting, which effectively achieves a similar position.

Treatments for anismus include biofeedback retraining, botox injections, and surgical resection. Anismus sometimes occurs together with other conditions that limit (see contraindication) the choice of treatments. Thus, thorough evaluation is recommended prior to treatment.

Biofeedback training for treatment of anismus is highly effective and considered the gold standard therapy by many.

Others however, reported that biofeedback had a limited therapeutic effect.

Injections of botulin toxin type-A into the puborectalis muscle are very effective in the short term, and somewhat effective in the long term. Injections may be helpful when used together with biofeedback training.

Historically, the standard treatment was surgical resection of the puborectalis muscle, which sometimes resulted in fecal incontinence. Recently, partial resection (partial division) has been reported to be effective in some cases.

A method for repairing long-gap esophageal atresia using magnets has been developed, that does not require replacing the missing section with grafts of the intestine or other body parts. Using electromagnetic force to attract the upper and lower ends of the esophagus together was first tried in the 1970s by using steel pellets attracted to each other by applying external electromagnets to the patient. In the 2000s a further refinement was developed by Mario Zaritzky's group and others. The newer method uses permanent magnets and a balloon.

1. The magnets are inserted into the upper pouch via the baby's mouth or nose, and the lower via the gastrotomy feeding tube hole (which would have had to be made anyway to feed the baby, therefore not requiring any additional surgery).

2. The distance between the magnets is controlled by a balloon in the upper pouch, between the end of the pouch and the magnet. This also controls the force between the magnets so it is not strong enough to cause damage.

3. After the ends of the esophagus have stretched enough to touch, the upper magnet is replaced by one without a balloon and the stronger magnetic attraction causes the ends to fuse (anastomosis).

In April 2015 Annalise Dapo became the first patient in the United States to have their esophageal atresia corrected using magnets.

Surgery is often required to prevent further damage to the anal sphincters. The goals of surgery are to restore the normal anatomy and to minimize symptoms. There is no globally agreed consensus as to which procedures are more effective, and there have been over 50 different operations described.

Surgical approaches in rectal prolapse can be either perineal or abdominal. A perineal approach (or trans-perineal) refers to surgical access to the rectum and sigmoid colon via incision around the anus and perineum (the area between the genitals and the anus). Abdominal approach (trans-abdominal approach) involves the surgeon cutting into the abdomen and gaining surgical access to the pelvic cavity. Procedures for rectal prolapse may involve fixation of the bowel (rectopexy), or resection (a portion removed), or both. Trans-anal (endo-anal) procedures are also described where access to the internal rectum is gained through the anus itself.

Patients with abnormal cardiac and kidney function may be more at risk for hemolytic uremic syndrome