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.

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.

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.

Dietary modification may be important for successful management. Both diarrhea and constipation can contribute to different cases, so dietary advice must be tailored to address the underlying cause or it may be ineffective or counter productive. In persons with disease aggravated by diarrhea or those with rectal loading by soft stools, the following suggestions may be beneficial: increase dietary fiber; reduce wholegrain cereals/bread; reduce fruit and vegetables which contain natural laxative compounds (rhubarb, figs, prunes/plums); limit beans, pulses, cabbage and sprouts; reduce spices (especially chilli); reduce artificial sweeteners (e.g. sugar free chewing gum); reduce alcohol (especially stout, beer and ale); reduce lactose if there is some degree of lactase deficiency; and reduce caffeine. Caffeine lowers the resting tone of the anal canal and also causes diarrhea. Excessive doses of vitamin C, magnesium, phosphorus and/or calcium supplements may increase FI. Reducing olestra fat substitute, which can cause diarrhea, may also help.

Pharmacological management may include anti-diarrheal/constipating agents and laxatives/stool bulking agents Stopping or substituting any previous medication that causes diarrhea may be helpful in some (see table). There is not good evidence for the use of any medications however.

In people who have undergone gallbladder removal, the bile acid sequestrant cholestyramine may help minor degrees of FI. Bulking agents also absorb water, so may be helpful for those with diarrhea. A common side effect is bloating and flatulence. Topical agents to treat and prevent dermatitis may also be used, such as topical antifungals when there is evidence of perianal candidiasis or occasionally mild topical anti-inflammatory medication. Prevention of secondary lesions is carried out by perineal cleansing, moisturization, and use of a skin protectant.

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.

Treatment for fistula varies depending on the cause and extent of the fistula, but often involves surgical intervention combined with antibiotic therapy.

Typically the first step in treating a fistula is an examination by a doctor to determine the extent and "path" that the fistula takes through the tissue.

In some cases the fistula is temporarily covered, for example a fistula caused by cleft palate is often treated with a palatal obturator to delay the need for surgery to a more appropriate age.

Surgery is often required to assure adequate drainage of the fistula (so that pus may escape without forming an abscess). Various surgical procedures are commonly used, most commonly fistulotomy, placement of a seton (a cord that is passed through the path of the fistula to keep it open for draining), or an endorectal flap procedure (where healthy tissue is pulled over the internal side of the fistula to keep feces or other material from reinfecting the channel). Treatment involves filling the fistula with fibrin glue; also plugging it with plugs made of porcine small intestine submucosa have also been explored in recent years, with variable success. Surgery for anorectal fistulae is not without side effects, including recurrence, reinfection, and incontinence. High rate of recurrence and more chances of complications like incontinence are always there in fistula surgeries (Anal Fistula).

It is important to note that surgical treatment of a fistula without diagnosis or management of the underlying condition, if any, is not recommended. For example, surgical treatment of fistulae in Crohn's disease can be effective, but if the Crohn's disease itself is not treated, the rate of recurrence of fistula is very high (well above 50%).

Treatments range from recommendations for over-the-counter products to more invasive surgical procedures.

Among the most common outpatient advice given to patients with less severe disorders include a high-fiber diet, application of ointment, and increased water intake. More serious procedures include the removal of affected tissue, injection of botulinum toxin, or surgically opening the fistula tract in the sphincter muscle.

Fetal and neonatal intestinal atresia are treated using laparotomy after birth. If the area affected is small, the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for period of time, a temporary stoma may be placed.

Possible treatments include:

- In stable cases, use of laxatives and bulking agents, as well as modifications in diet and stool habits are effective.

- Corticosteroids and other anti-inflammatory medication is used in toxic megacolon.

- Antibiotics are used for bacterial infections such as oral vancomycin for "Clostridium difficile"

- Disimpaction of feces and decompression using anorectal and nasogastric tubes.

- When megacolon worsens and the conservative measures fail to restore transit, surgery may be necessary.

- Bethanechol can also be used to treat megacolon by means of its direct cholinergic action and its stimulation of muscarinic receptors which bring about a parasympathetic like effect.

There are several surgical approaches to treat megacolon, such as a colectomy (removal of the entire colon) with ileorectal anastomosis (ligation of the remaining ileum and rectum segments), or a total proctocolectomy (removal of colon, sigmoid and rectum) followed by ileostomy or followed by ileoanal anastomosis.

Treatment for proctitis varies depending on severity and the cause. For example, the physician may prescribe antibiotics for proctitis caused by bacterial infection. If the proctitis is caused by Crohn's disease or ulcerative colitis, the physician may prescribe the drug 5-aminosalicyclic acid (5ASA) or corticosteroids applied directly to the area in enema or suppository form, or taken orally in pill form. Enema and suppository applications are usually more effective, but some patients may require a combination of oral and rectal applications.

Another treatment available is that of fiber supplements such as Metamucil. Taken daily these may restore regularity and reduce pain associated with proctitis.

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.

Unlike oesophageal varices, rectal varices are less prone to bleeding, are less serious when a bleed does occur, and are easier to treat because of the more accessible location.

Typically, treatment consists of addressing the underlying portal hypertension. Some treatments include portosystemic shunting, ligation, and under-running suturing. Insertion of a transjugular intrahepatic portosystemic shunt (TIPS) has been shown to alleviate varices caused by portal hypertension. Successful treatment of portal hypertension that subsequently reduces anorectal varices provides a confirmation of the initial diagnosis, allowing for a distinction between varices and hemorrhoids, which would not have been alleviated by reduction of portal hypertension.

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.

The surgical treatment involves the resection of the extracranial venous package and ligation of the emissary communicating vein. In some cases of SP, surgical excision is performed for cosmetic reasons. The endovascular technique has been described by transvenous approach combined with direct puncture and the recently endovascular embolization with Onyx.

The main treatment for isolated epispadias is a comprehensive surgical repair of the genito-urinary area usually during the first 7 years of life, including reconstruction of the urethra, closure of the penile shaft and mobilisation of the corpora. The most popular and successful technique is known as the modified Cantwell-Ransley approach. In recent decades however increasing success has been achieved with the complete penile disassembly technique despite its association with greater and more serious risk of damage.

Head circumference measurements should be obtained regularly and monitored carefully to detect hydrocephalus. Neurosurgical procedures to relieve hydrocephalus are important. A ventriculoperitoneal shunt may be required in some infants. A pediatric cardiologist should be consulted to manage high-output failure, if present. Often patients need to be intubated. In most cases, the fistulous arteries feeding into the Vein of Galen must be blocked, thereby reducing the blood flow into the vein. Open surgery has a high morbidity and mortality. Recent advances over the past few decades have made endovascular embolization the preferred method of treatment. These treatments are preferred because they offer little threat to the surrounding brain tissue. However, there have been several reported cases of arteriovenous malformations recurring. The young age of many patients, the complex vascular anatomy, and the sensitive location of the Vein of Galen offer considerable challenges to surgeons. Another treatment option is Radiotherapy. Radiotherapy, also called radiosurgery, involves the use of focused beams to damage the blood vessel. Radiotherapy is often not pursued as a treatment because the effects of the procedure can take months or years and there is risk of damaging adjacent brain tissue.

Surgery is not always an option when the anatomy of the malformation creates too much of a risk. Recent improvements in endovascular procedures have made many cases, which were not surgically accessible, treatable. Endovascular treatments involve delivering drugs, balloons, or coils to the site of the malformation through blood vessels via catheters. These treatments work by limiting blood flow through the vein. There is, however, still risk of complications from endovascular treatments. The wall of the vein can be damaged during the procedure and, in some cases, the emboli can become dislodged and travel through the vascular system. Two-dimensional echocardiography with color-flow imaging and pulsed Doppler ultrasound was used to evaluate one fetus and five neonates with a Vein of Galen malformation. Color-flow imaging and pulsed Doppler ultrasonography provided anatomical and pathophysiological information regarding cardiac hemodynamics and intracranial blood flow; with the patient's clinical status, these methods provided a reliable, noninvasive means to evaluate the effectiveness of therapy and the need for further treatment in neonates with Vein of Galen malformations. When none of these procedures are viable, shunting can be used to ameliorate the pressure inside the varix. Seizures usually are managed with antiepileptic medications.

While there is no current cure, the treatments for Chiari malformation are surgery and management of symptoms, based on the occurrence of clinical symptoms rather than the radiological findings. The presence of a syrinx is known to give specific signs and symptoms that vary from dysesthetic sensations to algothermal dissociation to spasticity and paresis. These are important indications that decompressive surgery is needed for patients with Chiari Malformation Type II. Type II patients have severe brain stem damage and rapidly diminishing neurological response.

Decompressive surgery involves removing the lamina of the first and sometimes the second or third cervical vertebrae and part of the occipital bone of the skull to relieve pressure. The flow of spinal fluid may be augmented by a shunt. Since this surgery usually involves the opening of the dura mater and the expansion of the space beneath, a dural graft is usually applied to cover the expanded posterior fossa.

A small number of neurological surgeons believe that detethering the spinal cord as an alternate approach relieves the compression of the brain against the skull opening (foramen magnum), obviating the need for decompression surgery and associated trauma. However, this approach is significantly less documented in the medical literature, with reports on only a handful of patients. It should be noted that the alternative spinal surgery is also not without risk.

Complications of decompression surgery can arise. They include bleeding, damage to structures in the brain and spinal canal, meningitis, CSF fistulas, occipito-cervical instability and pseudomeningeocele. Rare post-operative complications include hydrocephalus and brain stem compression by retroflexion of odontoid. Also, an extended CVD created by a wide opening and big duroplasty can cause a cerebellar "slump". This complication needs to be corrected by cranioplasty.

In certain cases, irreducible compression of the brainstem occurs from in front (anteriorly or ventral) resulting in a smaller posterior fossa and associated Chiari malformation. In these cases, an anterior decompression is required. The most commonly used approach is to operate through the mouth (transoral) to remove the bone compressing the brainstem, typically the odontoid. This results in decompressing the brainstem and therefore gives more room for the cerebellum, thus decompressing the Chiari malformation. Arnold Menzes, MD, is the neurosurgeon who pioneered this approach in the 1970s at the University of Iowa. Between 1984 and 2008 (the MR imaging era), 298 patients with irreducible ventral compression of the brainstem and Chiari type 1 malformation underwent a transoral approach for ventral cervicomedullary decompression at the University of Iowa. The results have been excellent resulting in improved brainstem function and resolution of the Chiari malformation in the majority of patients.

Rectovestibular fistula is the most common defect of the rectum and anal canal in females.

Treatment for individuals with Dandy–Walker Syndrome generally consists of treating the associated problems, if needed.

A special tube (shunt) to reduce intracranial pressure may be placed inside the skull to control swelling. Endoscopic third ventriculostomy is also an option.

Treatment may also consist of various therapies such as occupational therapy, physiotherapy, speech therapy or specialized education. Services of a teacher of students with blindness/visual impairment may be helpful if the eyes are affected.

Anorectal anomalies are medical problems affecting the structure of the anus and rectum. A person with an anorectal problem would have some sort of deformative feature of the anus or rectum, collectively known as an anorectal malformation.

Examples of anorectal anomalies include:

- Anal stenosis

- Imperforate anus

- Proctitis

- Anal bleeding

- Anal fistula

- Anal cancer

- Anal itching

- Hemorrhoid (piles)

Anal stricture or anal stenosis is a narrowing of the anal canal. It can be caused by a number of surgical procedures including: hemorrhoid removal and following anorectal wart treatment.

A baby with a prenatally diagnosed cystic hygroma should be delivered in a major medical center equipped to deal with neonatal complications, such as a neonatal intensive care unit. An obstetrician usually decides the method of delivery. If the cystic hygroma is large, a cesarean section may be performed. After birth, infants with a persistent cystic hygroma must be monitored for airway obstruction. A thin needle may be used to reduce the volume of the cystic hygroma to prevent facial deformities and airway obstruction. Close observation of the baby by a neonatologist after birth is recommended. If resolution of the cystic hygroma does not occur before birth, a pediatric surgeon should be consulted.

Cystic hygromas that develop in the third trimester, after thirty weeks gestation, or in the postnatal period are usually not associated with chromosome abnormalities. There is a chance of recurrence after surgical removal of the cystic hygroma. The chance of recurrence depends on the extent of the cystic hygroma and whether its wall was able to be completely removed.

Treatments for removal of cystic hygroma are surgery or sclerosing agents which include:

- Bleomycin

- Doxycycline

- Ethanol (pure)

- Picibanil (OK-432)

- Sodium tetradecyl sulfate