Surgical treatments may be used to treat the condition, and include retro-rectal levatorplasty, post-anal repair, retro-anal levator plate myorrhaphy.

Hand-foot-genital syndrome is inherited in an autosomal dominant manner. The proportion of cases caused by de novo mutations is unknown because of the small number of individuals described. If a parent of the proband is affected, the risk to the siblings is 50%. When the parents are clinically unaffected, the risk to the sibs of a proband appears to be low. Each child of an individual with HFGS has a 50% chance of inheriting the mutation. Prenatal testing may be available through laboratories offering custom prenatal testing for families in which the disease-causing mutation has been identified in an affected family member.

Botulinum A toxin is a valuable alternative for patients who do not want surgical methods.

Hand-foot-genital syndrome (HFGS) is characterized by limb malformations and urogenital defects. Mild bilateral shortening of the thumbs and great toes, caused primarily by shortening of the distal phalanx and/or the first metacarpal or metatarsal, is the most common limb malformation and results in impaired dexterity or apposition of the thumbs. Urogenital abnormalities include abnormalities of the ureters and urethra and various degrees of incomplete Müllerian fusion in females and hypospadias of variable severity with or without chordee in males. Vesicoureteral reflux, recurrent urinary tract infections, and chronic pyelonephritis are common; fertility is normal.

Conservative treatment involves the long term use of laxatives and enemas, and has limited success. Dietary changes in order to control the disease are ineffective and high fiber diets often worsen the symptoms in children. As a last resort, surgical treatment (internal sphincter myectomy or colon resection) is used. In extreme cases, the only effective cure is a complete transplant of the affected parts.

A famous case of IND is that of Adele Chapman, who had a triple transplant of the small intestine, pancreas and liver, the first of its kind in the UK; therefore the official charity of IND is the Adele Chapman Foundation.

The condition mainly occurs in women, and it is thought by some to be one of the main defects encountered problem in perineology.

Prostheses are used for nonsurgical closure in a situation of velopharyngeal dysfunction. There are two types of prosthesis: the speech bulb and the palatal lift prosthesis. The speech bulb is an acrylic body that can be placed in the velopharyngeal port and can achieve obstruction. The palatal lift prosthesis is comparable with the speech bulb, but with a metal skeleton attached to the acrylic body. This will also obstruct the velopharyngeal port. It is a good option for patients that have enough tissue but a poor control of the coordination and timing of velopharyngeal movement. It is also used in patients with contraindications for surgery. It has also been used as a reversible test to confirm whether a surgical intervention would help.

Foix–Alajouanine syndrome is a disorder caused by an arteriovenous malformation of the spinal cord. The patients present with symptoms indicating spinal cord involvement (paralysis of arms and legs, numbness and loss of sensation and sphincter dysfunction), and pathological examination reveals disseminated nerve cell death in the spinal cord and abnormally dilated and tortuous vessels situated on the surface of the spinal cord. Surgical treatment can be tried in some cases. If surgical intervention is contraindicated, corticosteroids may be used.

The condition is named after Charles Foix and Théophile Alajouanine.

The main objective of physical treatment is to achieve adequate velopharyngeal (VP) function and normal oral-nasal resonance.

Cuffitis is treated with mesalamine suppositories or topical application of lidocaine or corticosteroid medications. Systemic medications are rarely used.

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.

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

Traditional remedies have ranged from warm baths (if the pain lasts long enough to draw a bath), warm to hot enemas, relaxation techniques, and various medications.

Yoga pose "downward facing dog" -Adho Mukha Svanasana, or modification from it seems to help to relax the muscles and ease the pain. The idea of the yoga pose is that the position will force the muscles to relax and therefore tension will relieve over time. Also relaxing one's jaw muscles will help to relax the muscles in rectal area, method used by women giving birth.

In patients who suffer frequent, severe, prolonged attacks, inhaled salbutamol has been shown in some studies to reduce their duration.

The use of botulinum toxin has been proposed as analgesic, and low dose diazepam at bedtime has been suggested as preventative.

The most common approach for mild cases is simply reassurance and topical treatment with calcium-channel blocker (diltiazem, nifedipine) ointment, salbutamol inhalation and sublingual nitroglycerine.For persistent cases, local anesthetic blocks, clonidine or Botox injections can be considered. Supportive treatments directed at aggravating factors include high-fiber diet, withdrawal of drugs which have gut effects (e.g., drugs that provoke or worsen constipation including narcotics and oral calcium channel blockers; drugs that provoke or worsen diarrhea including quinidine, theophylline, and antibiotics), warm baths, rectal massage, perineal strengthening exercises, anti-cholinergic agents, non-narcotic analgesics, sedatives or muscle relaxants such as diazepam.

Cloacas appear in a wide spectrum of variation in females born with the malformation. The single orifice, called a common channel, may occur varying in length from 1 to 10 cm. The length of the common channel can be used to judge prognostic outcomes and technical challenges during surgical repair. A common channel less than 3 cm in length usually has good sphincter muscles and a well-developed sacrum.

A 2014 meta-analysis of three small trials evaluating probiotics showed a slight improvement in management of chronic idiopathic constipation, but well-designed studies are necessary to know the true efficacy of probiotics in treating this condition.

Children with functional constipation often claim to lack the sensation of the urge to defecate, and may be conditioned to avoid doing so due to a previous painful experience. One retrospective study showed that these children did indeed have the urge to defecate using colonic manometry, and suggested behavioral modification as a treatment for functional constipation.

The incidence of VACTERL association is estimated to be approximately 1 in 10,000 to 1 in 40,000 live-born infants. It is seen more frequently in infants born to diabetic mothers. While most cases are sporadic, there are clearly families who present with multiple involved members.

3C syndrome, also known as CCC dysplasia, Craniocerebellocardiac dysplasia or Ritscher–Schinzel syndrome, is a rare condition, whose symptoms include heart defects, cerebellar hypoplasia, and cranial dysmorphism. It was first described in the medical literature in 1987 by Ritscher and Schinzel, for whom the disorder is sometimes named.

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.

High-voltage pulsed galvanic stimulation (HGVS) has been shown to be of prophylactic benefit, to reduce the incidence of attacks. The patient is usually placed in the left lateral decubitus position and a sterile probe is inserted into the anus. The negative electrode is used and the stimulator is set with a pulse frequency of 80 to 120 cycles per second. The voltage (intensity) is started at 0, progressively raised to a threshold of patient discomfort, and then is decreased to a level that the patient finds comfortable. As the patient's tolerance increases, the voltage can be gradually increased to 250 to 350 Volts. Each treatment session usually lasts between 15 and 60 minutes. Several studies have reported short-term success rates that ranged from 65 to 91%.

The pathophysiology of the condition results from neuronal plasticity associated with bladder afferents and motor neurons innervating the external urethral sphincter. People with this condition generally experience daytime and night time wetting, urinary retention, and often have a history of urinary tract and bladder infections. Constipation and encopresis are often associated with this condition.

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.

There is considerable research into the causes, diagnosis and treatments for FGIDs. Diet, microbiome, genetics, neuromuscular function and immunological response all interact. Heightened mast cell activation has been proposed to be a common factor among FGIDs, contributing to visceral hypersensitivity as well as epithelial, neuromuscular, and motility dysfunction.

The outcome of this disease is dependent on the severity of the cardiac defects. Approximately 1 in 3 children with this diagnosis require shunting for the hydrocephaly that is often a consequence. Some children require extra assistance or therapy for delayed psychomotor and speech development, including hypotonia.

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.