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.

Additional findings that may be present in HFGS according to the latest research are:

- Limited metacarpophalangeal flexion of the thumb or limited ability to oppose the thumb and fifth finger

- Hypoplastic thenar eminences

- Medial deviation of the great toe (hallux varus), a useful diagnostic sign when present

- Small great toenail

- Fifth-finger clinodactyly, secondary to a shortened middle phalanx

- Short feet

- Altered dermatoglyphics of the hands; when present, primarily involving distal placement of the axial triradius, lack of thenar or hypothenar patterning, low arches on the thumbs, thin ulnar loops (deficiency of radial loops and whorls), and a greatly reduced ridge count on the fingers

Radiographic findings

- Hypoplasia of the distal phalanx and first metacarpal of the thumbs and great toes

- Pointed distal phalanges of the thumb

- Lack of normal tufting of the distal phalanges of the great toes

- Fusions of the cuneiform to other tarsal bones or trapezium-scaphoid fusion of the carpals

- Short calcaneus

- Occasional bony fusions of the middle and distal phalanges of the second, third, fourth, or fifth toes

- Delayed carpal or tarsal maturation

- Metacarpophalangeal profile reflecting shortening of the first metacarpal, the first and second phalanges, and the second phalanx of the second and fifth digits

Urogenital Defects

Females may have the following:

- Vesicoureteral reflux secondary to ureteric incompetence

- Ectopic ureteral orifices

- Trigonal hypoplasia

- Hypospadiac urethra

- Subsymphyseal epispadias

- Patulous urethra

- Urinary incontinence (related to structural anomalies and weakness of the bladder sphincter muscle)

- Small hymenal opening

- Various degrees of incomplete Müllerian fusion with or without two cervices or a longitudinal vaginal septum

Males may have the following:

- Retrograde ejaculation (related to structural anomalies and weakness of the bladder sphincter muscle)

Abnormal descent of the perineum may be asymptomatic, but otherwise the following may feature:

- perineodynia (perineal pain)

- Colo-proctological symptoms, e.g. obstructed defecation, dyschesia (constipation), or degrees of fecal incontinence

- gynaecological symptoms, e.g. cystocele (prolapse of the bladder into the vagina) and rectocele (prolapse of the rectum into the vagina)

- lower urinary tract symptoms, e.g. dysuria (painful urination), dyspareunia (pain during sexual intercourse), urinary incontinence & urgency

Other researchers concluded that abnormal perineal descent did not correlate with constipation or perineal pain, and there are also conflicting reports of the correlation of fecal incontinence with this condition.

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

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.

The following features are observed with VACTERL association:

- V - Vertebral anomalies

- A - Anorectal malformations

- C - Cardiovascular anomalies

- T - Tracheoesophageal fistula

- E - Esophageal atresia

- R - Renal (Kidney) and/or radial anomalies

- L - Limb defects

Although it was not conclusive whether VACTERL should be defined by at least two or three component defects, it is typically defined by the presence of at least three of the above congenital malformations.

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 classical triad of symptoms that defines 3C syndrome includes certain heart defects, hypoplasia (underdevelopment) of the cerebellum, and cranial dysmorphisms, which can take various forms. The heart defects and cranial dysmorphisms are heterogeneous in individuals who are all classed as having Ritscher-Schinzel syndrome.

Heart defects commonly seen with Ritscher-Schinzel syndrome are associated with the endocardial cushion and are the most important factor in determining a diagnosis. The mitral valve and tricuspid valve of the heart can be malformed, the atrioventricular canal can be complete instead of developing into the interatrial septum and interventricular septum, and conotruncal heart defects, which include tetralogy of Fallot, double outlet right ventricle, transposition of the great vessels, and hypoplastic left heart syndrome. Aortic stenosis and pulmonary stenosis have also been associated with 3C syndrome.

The cranial dysmorphisms associated with 3C syndrome are heterogeneous and include a degree of macrocephaly, a large anterior fontanel, a particularly prominent occiput and forehead, ocular hypertelorism (wide-set eyes), slanted palpebral fissures, cleft palate, a depressed nasal bridge, cleft palate with associated bifid uvula, low-set ears, micrognathia (an abnormally small jaw), brachycephaly (flattened head), and ocular coloboma. Low-set ears are the most common cranial dysmorphism seen in 3C syndrome, and ocular coloboma is the least common of the non-concurrent symptoms (cleft lip co-occurring with cleft palate is the least common).

Cranial dysplasias associated with 3C syndrome are also reflected in the brain. Besides the cerebellar hypoplasia, cysts are commonly found in the posterior cranial fossa, the ventricles and the cisterna magna are dilated/enlarged, and Dandy-Walker malformation is present. These are reflected in the developmental delays typical of the disease. 75% of children with 3C syndrome have Dandy-Walker malformation and hydrocephalus.

Signs and symptoms in other body systems are also associated with 3C syndrome. In the skeletal system, ribs may be absent, and hemivertebrae, syndactyly (fusion of fingers together), and clinodactyly (curvature of the fifth finger) may be present. In the GI and genitourinary systems, anal atresia, hypospadia (misplaced urethra), and hydronephrosis may exist. Adrenal hypoplasia and growth hormone deficiency are associated endocrine consequences of Ritscher-Schinzel syndrome. Some immunodeficiency has also been reported in connection with 3C syndrome.

Many children with the disorder die as infants due to severe congenital heart disease. The proband of Ritscher and Schinzel's original study was still alive at the age of 21.

A fetus with 3C syndrome may have an umbilical cord with one umbilical artery instead of two.

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.

Renal (kidney) defects are seen in approximately 50 percent of patients with VACTERL association. In addition, up to 35 percent of patients with VACTERL association have a single umbilical artery (there are usually two arteries and one vein) which is often associated with additional kidney or urologic problems. Renal abnormalities in VACTERL association can be severe, with incomplete formation of one or both kidneys or urologic abnormalities such as obstruction of outflow of urine from the kidneys or severe reflux (backflow) of urine into the kidneys from the bladder. These problems can cause kidney failure early in life and may require kidney transplant. Many of these problems can be corrected surgically before any damage can occur.

Individuals affected by AAA have adrenal insufficiency/Addison's disease due to ACTH resistance, alacrima (absence of tear secretion), and achalasia (a failure of a ring of muscle fibers, such as a sphincter, to relax) of the lower esophageal sphincter at the cardia which delays food going to the stomach and causes dilation of the thoracic esophagus. There may also be signs of autonomic dysfunction with AAA, such as pupillary abnormalities, an abnormal reaction to intradermal histamine, abnormal sweating, orthostatic hypotension, and disturbances of the heart rate. Hypoglycemia (low blood sugar) is often mentioned as an early sign. The disorder has also been associated with mild mental retardation.

The syndrome is highly variable. Managed effectively, affected individuals can have a normal lifespan and bear children.

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.

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.

A persistent cloaca is a symptom of a complex anorectal congenital disorder, in which the rectum, vagina, and urinary tract meet and fuse, creating a cloaca, a single common channel.

Triple-A syndrome or AAA syndrome, also known as achalasia-addisonianism-alacrima syndrome or Allgrove syndrome, is a rare autosomal recessive congenital disorder. In most cases, there is no family history of it. The syndrome was first identified by Jeremy Allgrove and colleagues in 1978. The syndrome involves achalasia, addisonianism (adrenal insufficiency of primary type), and alacrima (insufficiency of tears). Alacrima is usually the earliest manifestation. It is a progressive disorder that can take years to develop the full blown clinical picture.

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.

Diagnosis of a female with cloaca should be suspected in a female born with an imperforate anus and small looking genitalia. The diagnosis can be made clinically. Failure to identify a cloaca as being present in a newborn may be dangerous, as more than 90% have associated urological problems. The goal for treatment of a female born with cloaca is to achieve bowel control, urinary control, and sexual function, which includes menstruation, sexual intercourse, and possibly pregnancy. Cloacas probably occur in 1 in 20,000 live births.

Bladder sphincter dyssynergia (also known as detrusor sphincter dysynergia (DSD) (the ICS standard terminology agreed 1998) and neurogenic detrusor overactivity (NDO)) is a consequence of a neurological pathology such as spinal injury or multiple sclerosis. which disrupts central nervous system regulation of the micturition (urination) reflex resulting in dyscoordination of the detrusor muscles of the bladder and the male or female external urethral sphincter muscles. In normal lower urinary tract function, these two separate muscle structures act in synergistic coordination. But in this neurogenic disorder, the urethral sphincter muscle, instead of relaxing completely during voiding, dyssynergically contracts causing the flow to be interrupted and the bladder pressure to rise.

There are several forms of imperforate anus and anorectal malformations. The new classification is in relation of the type of associated fistula.

The classical Wingspread classification was in low and high anomalies:

- A low lesion, in which the colon remains close to the skin. In this case, there may be a stenosis (narrowing) of the anus, or the anus may be missing altogether, with the rectum ending in a blind pouch.

- A high lesion, in which the colon is higher up in the pelvis and there is a fistula connecting the rectum and the bladder, urethra or the vagina.

- A persistent cloaca (from the term cloaca, an analogous orifice in reptiles and amphibians), in which the rectum, vagina and urinary tract are joined into a single channel.

Imperforate anus is usually present along with other birth defects—spinal problems, heart problems, tracheoesophageal fistula, esophageal atresia, renal anomalies, and limb anomalies are among the possibilities.

Symptoms of cuffitis mimic those of pouchitis. In addition, patients with cuffitis often present with small volume bloody bowel movements. Often, cuffitis can produce the appearance of bright red blood on tissue.

Imperforate anus is associated with an increased incidence of some other specific anomalies as well, together being called the VACTERL association:

- V – Vertebral anomalies

- A – "Anal atresia"

- C – Cardiovascular anomalies

- T – Tracheoesophageal fistula

- E – Esophageal atresia

- R – Renal (kidney) and/or radial anomalies

- L – Limb defects

Other entities associated with an imperforate anus are trisomies 18 and 21, the cat-eye syndrome (partial trisomy or tetrasomy of a maternally derived number 22 chromosome), Baller-Gerold syndrome, Currarino syndrome, caudal regression syndrome, FG syndrome, Johanson-Blizzard syndrome, McKusick-Kaufman syndrome, Pallister-Hall syndrome, short rib-polydactyly syndrome type 1, Townes-Brocks syndrome, 13q deletion syndrome, urorectal septum malformation sequence, and the OEIS complex (omphalocele, exstrophy of the cloaca, imperforate anus, spinal defects).

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)

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.

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.

Signs and symptoms include:

- history of a protruding mass.

- degrees of fecal incontinence, (50-80% of patients) which may simply present as a mucous discharge.

- constipation (20-50% of patients) also described as tenesmus (a sensation of incomplete evacuation of stool) and obstructed defecation.

- a feeling of bearing down.

- rectal bleeding

- diarrhea and erratic bowel habits.

Initially, the mass may protrude through the anal canal only during defecation and straining, and spontaneously return afterwards. Later, the mass may have to be pushed back in following defecation. This may progress to a chronically prolapsed and severe condition, defined as spontaneous prolapse that is difficult to keep inside, and occurs with walking, prolonged standing, coughing or sneezing (Valsalva maneuvers). A chronically prolapsed rectal tissue may undergo pathological changes such as thickening, ulceration and bleeding.

If the prolapse becomes trapped externally outside the anal sphincters, it may become strangulated and there is a risk of perforation. This may require an urgent surgical operation if the prolapse cannot be manually reduced. Applying granulated sugar on the exposed rectal tissue can reduce the edema (swelling) and facilitate this.