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.

Diagnosis is based on physical examination including radiographs of the hands and feet and imaging studies of the kidneys, bladder, and female reproductive tract. HOXA13 is the only gene known to be associated with HFGS. Approximately 60% of mutations are polyalanine expansions. Molecular genetic testing is clinically available.

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

One of the main causes is suggested to be excessive and repetitive straining during defecation. Other causes include weakness of the pelvic floor muscles (secondary to age related neuropathic degeneration or traumatic injury during pregnancy and labor.

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.

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

Velopharyngeal insufficiency (VPI) is a failure of the body's ability to temporarily close the communication between the nasal cavity and the mouth, because of an anatomic dysfunction of the soft palate or of the lateral or posterior wall of the pharynx.

The effect of such a dysfunction leads to functional problems with speech (hypernasality), eating (chewing and swallowing), and breathing. This gap can be treated surgically, although the choice of operational technique is still controversial.

The terms velopharyngeal "incompetence", "inadequacy" and "insufficiency" historically have often been used interchangeably, although they do not necessarily mean the same thing (sense distinctions can be made but sometimes are not). Velopharyngeal insufficiency includes any structural defect of the velum or pharyngeal walls at the level of the nasopharynx with insufficient tissue to accomplish closure, or there is some kind of mechanical interference with closure. It is important that the term insufficiency is used if it is an anatomical defect and not a neurological problem.

Velopharyngeal insufficiency (VPI) can be caused by a variety of disorders (structural, genetic, functional or acquired) and is very often associated with a cleft palate. Abnormal physiological separation of the oropharynx from the nasopharynx can lead to VPI and hypernasality.

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.

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.

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

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.

An incorrect diagnosis can lead to insufficient differential management. Most surgeons have their own vision on diagnosis and differential management. If it is thought, for instance, that palatal length is the only variable necessary for achieving normal closure, differential management will be insufficient. Therefore, differential diagnosis is important, because otherwise treatment of the velopharynx may not be appropriate.

There is not one single operative approach to VPI because anatomical structures diverge a lot between individuals. With diagnostic tools the surgeon is able to decide which technique should be used based on the anatomical situation of the individual. The goal of every operation is to achieve the best possible result with the technique assigned to each individual case.

Several methods can be used to diagnose velopharyngeal inadequacy.

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.

It can be grouped into NID A and NID B, with the "A" form affecting the sympathetic innervation, and the "B" version affecting the parasympathetic innervation.

In 2002 Martucciello G et al. published the first analysis of associated anomalies in IND population is an important clinical approach to investigate possible pathogenetic correlations. Two recessive syndromes were identified (3 families). The first was characterized by NID B, intestinal malrotation, and congenital short bowel, the second by NID B, short stature, mental retardation, and facial dysmorphism. In this study, gastrointestinal anomalies accounted for 67.4% of all associated disorders. These data suggest a strong correlation between IND and intestinal development.

3C syndrome is very rare, occurring in less than 1 birth per million. Because of consanguinity due to a founder effect, it is much more common in a remote First Nations village in Manitoba, where 1 in 9 people carries the recessive gene.

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.

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.

Intestinal neuronal dysplasia (or neuronal intestinal dysplasia or NID) is an inherited disease of the intestine that affects one in 3000 children and adults. The intestine uses peristalsis to push its contents toward the anus; IND sufferers have a problem with the motor neurons that lead to the intestine, inhibiting this process and thus preventing digestion.

It can often be confused for Hirschsprung's disease, as both have similar symptoms.

FI is thought to be very common, but much under-reported due to embarrassment. One study reported a prevalence of 2.2% in the general population. It affects people of all ages, but is more common in older adults (but it should not be considered a normal part of aging). Females are more likely to develop it than males (63% of those with FI over 30 may be female). In 2014, the National Center for Health Statistics reported that one out of every six seniors in the U.S. who lived in their own home or apartment had FI. Men and women were equally affected. 45–50% of people with FI have severe physical and/or mental disabilities.

Risk factors include age, female gender, urinary incontinence, history of vaginal delivery (non-Caesarean section childbirth), obesity, prior anorectal surgery, poor general health and physical limitations. Combined urinary and fecal incontinence is sometimes termed double incontinence, and it is more likely to be present in those with urinary incontinence.

Traditionally, FI was thought to be an insignificant complication of surgery, but it is now known that a variety of different procedures are associated with this possible complication, and sometimes at high levels. Examples are midline internal sphincterotomy (8% risk), lateral internal sphincterotomy, fistulectomy, fistulotomy (18-52%), hemorrhoidectomy (33%), ileo-anal reservoir reconstruction, lower anterior resection, total abdominal colectomy, ureterosigmoidostomy, and anal dilation (Lord's procedure, 0-50%). Some authors consider obstetric trauma to be the most common cause.

Imperforate anus has an estimated incidence of 1 in 5000 births. It affects boys and girls with similar frequency. However, imperforate anus will present as the low version 90% of the time in females and 50% of the time in males.

Imperforate anus is an occasional complication of sacrococcygeal teratoma.

Surgery-associated ischemia may contribute inflammation at the anal transitional zone.

Patients whose cuffitis is refractory to mesalamine and/or corticosteroids should be evaluated for other disease in the cuff area, such as fistula or anastomotic leaks. Cuffitis that is refractory to medication can also be a sign of Crohn's disease of the pouch.

Chronic cuffitis can also contribute to the development of anastomotic stricture.

Cuffitis that is refractory, Crohn's-related, or is associated with surgical complications can contribute to pouch failure.

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.

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

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)

Cuffitis is inflammation at the anal transition zone or “cuff” created as a result of ileal pouch-anal anastomosis (IPAA). It is considered a variant form of ulcerative colitis that occurs in the rectal cuff. Cuffitis is a common complication of IPAA, particularly when a stapled anastomosis without mucosectomy procedure has been used.