Anorectal Malformation

An anorectal malformation (also called imperforate anus) is a birth defect that occurs early in pregnancy and that affects the development of the rectum and anus.  With this defect, the baby’s anal opening (where stool exits) and the rectum (the last part of the large intestine) do not develop properly, preventing the child from having normal bowel movements.

The abnormalities can appear differently such that any of the following can occur:  1) The anal opening may be absent and may end as a closed pouch inside the body. 2) The anal opening may be too small or in the incorrect location which can lead to painful bowel movements or severe constipation. 3) The anal opening may be absent and instead a connection forms between the end of the rectum and other structures (genital or urinary systems).  When a connection forms between the end of the bowel and the genitourinary system or the skin on the perineum, it is called a fistula.

Abnormal development of the anus and rectum are often accompanied by abnormalities of the genital system and the urinary system.  The most complex of these is called a cloaca. A cloaca is a malformation in which the rectum, vagina, and urinary tracts meet in a common channel that drains out of the body. In girls born with cloaca, only one opening will be visible in the perineum compared to the normal anatomy which has 3 separate openings.

Abnormal structural development of the bowel is accompanied by disordered formation and function of the muscles and nerves of the pelvic floor that tell the body when it’s “time to go”. This disordered formation can lead to stool and urinary incontinence.

Workup for ARM

After birth, babies are examined to ensure that the newborn’s anus is open and in the correct position. If the anal opening is absent or in the wrong spot, the doctor will look for stool coming out of the urethra, vagina, vestibule (area between the labia behind the vaginal opening), or skin near the expected anal position (usually anterior to the normal location) within the first 48 hours after birth. If stool passes from an abnormal location or no anus is identified, the doctor will do a number of tests to better understand the anorectal abnormality.  Other medical tests will also be performed to evaluate for any associated anomalies involving the heart, genitourinary system, spine and spinal cord. These studies might be:

  • X-rays of the pelvic area to show how far the rectum reaches, and to see if there are any problems with the way the lower spine has developed.
  • Abdominal and pelvic ultrasounds to examine the urinary tract more closely looking for blockages or abnormal fluid collections. Sometimes an additional test, a voiding cystourethrogram (VCUG) will be performed for further examination of the urinary tract. In girls, an ultrasound will also evaluate the vagina and uterus.
  • Spinal ultrasound to look for a tethered cord. An untreated tethered cord can lead to neurologic problems, such as bowel or bladder dysfunction and leg weakness as the child grows. If the spinal ultrasound shows any abnormalities, an MRI of the spine will be ordered to further define the baby’s anatomy.
  • Echocardiogram to look for any heart defects
Surgery for ARM

Once an anorectal malformation is identified, surgical planning for correction of the abnormality will begin. There are a few general courses for surgery, depending on the child’s anatomy.

  • Incorrect location of anal opening in skin on the bottom with draining stool- In this case, considered a ‘low’ abnormality, a single operation can be performed to create an anal opening in the correct position within the anal sphincter. This procedure often occurs within a few days to few months after birth.
  • Rectum does not reach the skin, but is found low near anal sphincter- This is also considered a ‘low’ abnormality and can often be performed in a single operation where an anal opening is made in the correct position, within the anal sphincter. This procedure often occurs within a few days after birth. This may also be treated initially with a colostomy (see “c” below) to allow stool to pass with the corrective surgery delayed for several months.
  • Rectum does not reach the skin and is not present near the anal sphincter- This is considered to be a ‘high’ lesion.  The complete surgical repair will be done in three different operations. With complex malformations such as these, the baby is allowed to grow in order to make the surgery easier and safer.  First a colostomy is created.  This surgery usually happens in the first day or two after birth. A colostomy connects the end of the colon to the abdominal wall skin to allow stool to pass into a pouch outside of the body. A second opening is created at this same operation and is called the mucous fistula. The mucous fistula allows the blind end of the rectum to drain fluid or mucous as needed. The child will go home to recover from this operation.
  • Before the second operation, contrast will be put into the mucous fistula and x-rays will be taken to determine if a connection (fistula) to the genitourinary tract is present. Knowing where the fistula connects to the genitourinary tract and how far the blind end of the bowel is to the anal sphincter is essential for surgical planning.  After this study, the second operation will close the fistula to the genitourinary tract and will create an anal opening in the correct location, within the anal sphincter. The colostomy will be left intact at this operation, and not closed, to allow for adequate healing of the new anal opening. The child will go home to recover from this operation.  While at home, anal dilations (passing of a small, smooth rod into the newly created anus to gently stretch the opening) are an important part of recovery. Anal dilations help keep the newly created anus from getting narrow as it heals. Dilations are needed every day for several weeks.
  • The colostomy will be closed in a third operation a few months later after the new anus has shown to be well healed.
  • During this time, children may also need surgery for associated malformations. Surgical timing of both the anorectal malformation and other associated anomalies will require coordination amongst all involved surgical teams.
Conditions associated with ARM (GU, GI, GYN, Neurosurgical, Cardiac, Limb anomalies)

Commonly other abnormalities are noted in babies born with imperforate anus. These associated anomalies are grouped in the term: VACTERL.

VACTERL problems include:

  • V:Vertebral (including bony spine and/or the spinal cord)
  • A:Anus (anorectal malformation)
  • C:Cardiac (heart)
  • T/E:trachea (windpipe)/esophagus (swallowing tube)
  • R:Renal (including kidney, bladder, and reproductive organs)
  • L:Limbs (including arms and/or legs)


  • Vertebral:Problems can include bony abnormalities seen on x-ray that may not cause long term problems or may result in scoliosis if missing vertebrae (bones) or parts of vertebrae occur. The formation of the sacrum can also be abnormal. If the sacrum fails to form correctly, the nerves that control urinary and bowel function are generally also incorrectly formed.  The spinal cord can be affected by structural abnormalities or tethering of the spinal cord (bound by a connection to base of bony spine). These abnormalities need to be evaluated by a neurosurgeon and surgery may or may not be required.
  • Anus: Anorectal malformation as discussed above.
  • Cardiac:Congenital heart defects are the most common type of major birth defect associated with anorectal malformations. The type of and severity of cardiac defect needs to be evaluated by a cardiologist and may affect the timing of the anal reconstruction.
  • Esophageal Atresia/ Tracheoesophageal Fistula:Esophageal atresia is a defect in which the upper esophagus ends and does not connect with the lower esophagus and stomach. A Tracheoesophageal fistula (TEF) is when the esophagus connects with the trachea. This defect is typically ruled out by passage of a nasogastric tube following delivery.
  • Renal/Genitourinary: Urinary tract abnormalities are noted in approximately half of children born with anorectal malformations. The external genitourinary tract will be examined at birth looking for abnormalities. An ultrasound is subsequently performed shortly after birth to assess for potential internal abnormalities such as malformed or missing kidneys, abnormal fluid collections or signs of poor kidney drainage.  If abnormalities of the urinary system are noted at birth, often a voiding cystourethrogram (VCUG) will be performed. Close follow-up, often with repeated ultrasounds, is needed as the child grows.
  • Internal Female Structural Anomalies:As the gastrointestinal and urologic system develop in the developing female fetus, the uterus, fallopian tubes, and upper part of the vagina, grow and develop at the same time and develop from similar tissue.  Because of this, girls with ARM are at increased risk of having abnormalities in their reproductive system.  If present, these abnormalities are most commonly a vaginal septum (extra tissue in the vagina) or uterine anomaly.   Assessment of the female reproductive tract is an important part of the initial assessment and may involve both physical examination and radiologic studies.  The most severe ARM is called a cloaca. When a cloacal abnormality occurs, the rectum, urethra and vagina share a common pathway to the perineum. Girls with a cloacal anomaly will have one opening on the perineum rather than the normal 3 openings. Girls with a cloacal malformation may have a normal uterus, but are at increased risk of having abnormalities in their uterine structures such as  duplicated uteri, uterine cavities that are not fully developed and are not connected to the vagina, or no uterus at all. During the initial evaluation and repair, preliminary assessment of the female reproductive tract will be made, but it is important to carefully follow these girls as their internal reproductive system grows and develops to make sure we fully understand their anatomy and how its functioning.  Girls will often be followed with either pelvic ultrasound or MRI as they mature.  The good news is that there is no increased risk of problems with the ovaries, even if they are not visualized easily on pelvic ultrasound or MRI when patients are young.