If a colostomy is not performed immediately after birth, patients with rectovestibular fistulae may present later in life with complications including severe constipation and megacolon (abnormal dilation of the colon), requiring colostomy or further surgery.

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.

Affected newborns may present with acute urinary retention. In adolescent females, the most common symptoms of an imperforate hymen are cyclic pelvic pain and amenorrhea; other symptoms associated with hematocolpos include urinary retention, constipation, back pain, nausea, and diarrhea.

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)

The diagnosis of a rectovestibular fistula can be made in female newborns if the vulva is stained with meconium (the earliest form of stool in an infant). The opening of the anus may be difficult to see due to its small size and position, but it may be visible as a thickening of the median perineal raphe with an obvious anal dimple. Patients with rectovestibular fistulae are commonly misdiagnosed with rectovaginal fistulae.

Anal fistulae can present with the following symptoms:

- skin maceration

- pus, serous fluid and/or (rarely) feces discharge — can be bloody or purulent

- pruritus ani — itching

- depending on presence and severity of infection:

An imperforate hymen is a congenital disorder where a hymen without an opening completely obstructs the vagina. It is caused by a failure of the hymen to perforate during fetal development. It is most often diagnosed in adolescent girls when menstrual blood accumulates in the vagina and sometimes also in the uterus. It is treated by surgical incision of the hymen.

Symptoms include:

- Straining during defecation

- Mucous rectal discharge

- Rectal bleeding

- Sensation of incomplete evacuation (tenesmus)

- constipation, or more rarely diarrhea

- fecal incontinence (rarely)

A rectovaginal fistula is a medical condition where there is a fistula or abnormal connection between the rectum and the vagina.

Rectovaginal fistula may be extremely debilitating. If the opening between the rectum and vagina is wide it will allow both flatulence and feces to escape through the vagina, leading to fecal incontinence. There is an association with recurrent urinary and vaginal infections. The fistula may also connect the rectum and urethra, which is called recto-urethral fistula. Either conditions can lead to labial fusion. This type of fistula can cause pediatricians to misdiagnose imperforate anus. The severity of the symptoms will depend on the size of fistula. Most often, it appears after about one week or so after delivery.

Depending on their relationship with the internal and external sphincter muscles, fistulae are classified into five types:

- Extrasphincteric fistulae begin at the rectum or sigmoid colon and proceed downward, through the levator ani muscle and open into the skin surrounding the anus. Note that this type does not arise from the dentate line (where the anal glands are located). Causes of this type could be from a rectal, pelvic or supralevator origin, usually secondary to Crohn's disease or an inflammatory process such as appendiceal or diverticular abscesses.

- Suprasphincteric fistulae begin between the internal and external sphincter muscles, extend above and cross the puborectalis muscle, proceed downward between the puborectalis and levator ani muscles, and open an inch or more away from the anus.

- Transphincteric fistulae begin between the internal and external sphincter muscles or behind the anus, cross the external sphincter muscle and open an inch or more away from the anus. These may take a 'U' shape and form multiple external openings. This is sometimes termed a 'horseshoe fistula.'

- Intersphincteric fistulae begin between the internal and external sphincter muscles, pass through the internal sphincter muscle, and open very close to the anus.

- Submucosal fistulae pass superficially beneath the submucosa and do not cross either sphincter muscle.

Solitary rectal ulcer syndrome (SRUS, SRU), is a disorder of the rectum and anal canal, caused by straining and increased pressure during defecation. This increased pressure causes the anterior portion of the rectal lining to be forced into the anal canal (an internal rectal intussusception). The lining of the rectum is repeatedly damaged by this friction, resulting in ulceration. SRUS can therefore considered to be a consequence of internal intussusception (a sub type of rectal prolapse), which can be demonstrated in 94% of cases. It may be asymptomatic, but it can cause rectal pain, rectal bleeding, rectal malodor, incomplete evacuation and obstructed defecation (rectal outlet obstruction).

Atresia is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent.

Examples of atresia include:

- Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.

- Choanal atresia, blockage of the back of the nasal passage, usually by abnormal bony or soft tissue.

- Esophageal atresia, which affects the alimentary tract and causes the esophagus to end before connecting normally to the stomach.

- Imperforate anus, malformation of the opening between the rectum and anus.

- Intestinal atresia, malformation of the intestine, usually resulting from a vascular accident in utero.

- Microtia, absence of the ear canal or failure of the canal to be tubular or fully formed (can be related to Microtia, a congenital deformity of the pinna, or outer ear).

- Ovarian follicle atresia, the degeneration and subsequent resorption of one or more immature ovarian follicles.

- Potter sequence, congenital decreased size of the kidney leading to absolutely no functionality of the kidney, usually related to a single kidney.

- Pulmonary atresia, malformation of the pulmonary valve in which the valve orifice fails to develop.

- Renal agenesis, only having one kidney.

- Tricuspid atresia, a form of congenital heart disease whereby there is a complete absence of the tricuspid valve, and consequently an absence of the right atrioventricular connection.

- Vaginal atresia, a congenital occlusion of the vagina or subsequent adhesion of the walls of the vagina, resulting in its occlusion.

Other birth defects may co-exist, particularly in the heart, but sometimes also in the anus, spinal column, or kidneys. This is known as VACTERL association because of the involvement of Vertebral column, Anorectal, Cardiac, Tracheal, Esophageal, Renal, and Limbs. It is associated with polyhydramnios in the third trimester.

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.

Any attempt at feeding could cause aspiration pneumonia as the milk collects in the blind pouch and overflows into the trachea and lungs. Furthermore, a fistula between the lower esophagus and trachea may allow stomach acid to flow into the lungs and cause damage. Because of these dangers, the condition must be treated as soon as possible after birth.

Rectovaginal fistulas are often the result of trauma during childbirth (in which case it is known as obstetric fistula) where improper medical interventions are used, such as episiotomy with forceps/vacuum extraction or in situations where there is inadequate health care, such as in some developing countries. Rectovaginal fistula is said to be known as the leading cause in maternal death in developing countries. Risk factors include prolonged labour, difficult instrumental delivery and paramedian episiotomy. Rates in Eritrea are estimated as high as 350 per 100,000 vaginal births. Fistulas can also develop as a result of physical trauma to either the vagina or anus, including from rape. Women with rectovaginal fistulae are often stigmatized in developing countries, and become outcasts.

Rectovaginal fistula can also be a symptom of various diseases, including infection by lymphogranuloma venereum, or the unintended result of surgery, such as episiotomy or sexual reassignment surgery. They may present as a complication of vaginal surgery, including vaginal hysterectomy. They are a recognized presentation of rectal carcinoma or rarely diverticular disease of the bowel or Crohn's disease. They are seen rarely after radiotherapy treatment for cervical cancer.

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.

The sac, which is formed from an outpouching of peritoneum, protrudes in the midline, through the umbilicus (navel).

It is normal for the intestines to protrude from the abdomen, into the umbilical cord, until about the tenth week of pregnancy, after which they return to inside the fetal abdomen.

The omphalocele can be mild, with only a small loop of intestines present outside the abdomen, or severe, containing most of the abdominal organs. In severe cases surgical treatment is made more difficult because the infant's abdomen is abnormally small, having had no need to expand to accommodate the developing organs.

Larger omphalocele are associated with a higher risk of cardiac defects.

Mild cases may simply produce a sense of pressure or protrusion within the vagina, and the occasional feeling that the rectum has not been completely emptied after a bowel movement. Moderate cases may involve difficulty passing stool (because the attempt to evacuate pushes the stool into the rectocele instead of out through the anus), discomfort or pain during evacuation or intercourse, constipation, and a general sensation that something is "falling down" or "falling out" within the pelvis. Severe cases may cause vaginal bleeding, intermittent fecal incontinence, or even the prolapse of the bulge through the mouth of the vagina, or rectal prolapse through the anus. Digital evacuation, or, manual pushing, on the posterior wall of the vagina helps to aid in bowel movement in a majority of cases of rectocele. Rectocele can be a cause of symptoms of obstructed defecation.

Omphalocele, also spelled omphalocoele, is a rare abdominal wall defect in which the intestines, liver, and occasionally other organs remain outside of the abdomen in a sac because of failure of normal return of intestines and other contents back to abdominal cavity during around ninth week of intrauterine development.

Omphalocele occurs in 1/4,000 births and is associated with a high rate of mortality (25%) and severe malformations, such as cardiac anomalies (50%), neural tube defect(40%), exstrophy of bladder and Beckwith Wiedemann syndrome. Approximately 15% of live-born infants with omphalocele have chromosomal abnormalities. About 30% of infants with an omphalocele have other congenital abnormalities.

A rectocele ( ) or posterior vaginal wall prolapse results when the rectum herniates into or forms a bulge in the vagina. Two common causes of this defect is: childbirth, and hysterectomy. Rectocele also tends occur with other forms of pelvic organ prolapse such as enterocele, sigmoidocele and cystocele.

Although the term applies most often to this condition in females, males can also develop. Rectoceles in men are uncommon, and associated with prostatectomy.

Hydrocolpos is the distension of the vagina caused by accumulation of fluid due to congenital vaginal obstruction. The obstruction is often caused by an imperforate hymen or less commonly a transverse vaginal septum. The fluid consists of cervical and endometrial mucus or in rare instances urine accumulated through a vesicovaginal fistula proximal to the obstruction. In some cases it is associated with Bardet-Biedl Syndrome. If it occurs in prepubertal girls, it may show up as abdominal swelling. It may be detected by using ultrasound. It may also present at birth as a distended lower abdomen and vagina. It also associated with vaginal atresia.

Cloacal exstrophy (EC) is a severe birth defect wherein much of the abdominal organs (the bladder and intestines) are exposed. It often causes the splitting of both male and female genitalia (specifically, the penis and clitoris respectively), and the anus is occasionally sealed.

Cloacal exstrophy is a rare birth defect, present in 1/200,000 pregnancies and 1/400,000 live births.

It is caused by a defect of the ventral body wall—mesodermal migration is inhibited and folding fails.

Symptoms and signs in the newborn can be sepsis, abdominal mass, and respiratory distress. Other abdominopelvic or perineal congenital anomalies frequently prompt radiographic evaluation in the newborn, resulting in a diagnosis of coincident vaginal atresia. Symptoms for vaginal atresia include cyclical abdominal pain, the inability to start having menstrual cycles, a small pouch or dimple where a vaginal opening should be, and pelvic mass when the upper vagina becomes filled with menstrual blood. Signs and symptoms of vaginal atresia or vaginal agenesis can often go unnoticed in females until they reach the age of menstruation. Women may also experience some form of abdominal pain or cramping.