Anorectal Malformations (Imperforate Anus)

What are anorectal malformations?

Anorectal malformations are birth defects of a child’s anus or rectum that interfere with the normal passage of stool. When the anus is completely blocked, the condition is called imperforate anus.

In children with anorectal malformations, the anus may be missing, blocked by a thin or thick layer of tissue, or more narrow than normal. In rare cases, the anus may be normal while the rectum is blocked or narrowed.

Many children with anorectal malformations have a fistula, or abnormal passage, between the rectum to another part of the body, such as the

In some children with anorectal malformations, the rectum and the urinary tract have the same opening. This abnormality is called a cloaca.

How common are anorectal malformations?

About 1 in every 5,000 babies is born with anorectal malformations.1

Who is more likely to be born with anorectal malformations?

Boys are slightly more likely than girls to be born with anorectal malformations.1

If parents have one child with an anorectal malformation, the chance that a future child will have the condition is 1 in 100, which is higher than the average risk of 1 in 5,000.1

What other health problems do children with anorectal malformations have?

Children with anorectal malformations may have birth defects that affect other parts of the body. These may include defects of the

In some cases, children with Down syndrome also have anorectal malformations.

What are the complications of anorectal malformations?

If anorectal malformations are not diagnosed and treated shortly after a baby is born, the baby may develop symptoms of intestinal obstruction, such as vomiting, bloating or visible swelling of the abdomen, and not being able to pass stool. Intestinal obstruction can lead to serious complications, such as a hole in the wall of the intestine called a perforation, serious infection, and sepsis.

After anorectal malformations have been treated with surgery, some people may have complications later in life such as

What are the signs of anorectal malformations?

When examining a newborn baby, doctors may find signs of anorectal malformations, such as

  • no visible anus
  • an anal opening that is not in the normal location
  • an anus that is tighter or more narrow than normal

In the first 24 hours after birth, babies with anorectal malformations may pass no stool or may pass stool through a fistula and out of the perineum, urethra, or vagina.

Babies with signs of anorectal malformation need medical treatment right away to prevent complications.

What causes anorectal malformations?

Anorectal malformations occur when the anus and rectum don’t develop normally before birth. Experts don’t know what causes problems with the development of the anus and rectum. However, genes or changes in genes—called mutations—may play a role.

How do doctors diagnose anorectal malformations?

Doctors diagnose anorectal malformations with a physical exam and imaging tests. They may also order tests to check for other health problems that are common in children with anorectal malformations.

Physical exam

Shortly after a baby is born, a doctor will examine the baby from head to toe. Doctors often diagnose anorectal malformations during this exam. Doctors will also examine the baby’s perineum and genitals and check for other birth defects.

Newborn baby being examined by a health care professional.
Doctors often diagnose anorectal malformations during a physical exam.

Imaging tests

Doctors may use the following tests to examine defects of the anus and rectum

  • ultrasound, which uses sound waves to create an image of organs
  • x-rays, which use a small amount of radiation to create pictures of the inside of the body
  • magnetic resonance imaging (MRI), which takes pictures of the body’s internal organs and soft tissues without using x-rays

How do doctors treat anorectal malformations?

Doctors treat anorectal malformations with surgery. The type of surgery depends on the location and type of malformation.

Doctors often perform surgery in the first few days after the baby is born. In some cases, doctors can repair the anorectal malformation with one operation. In other cases, doctors first perform a colostomy to attach the colon to a stoma, an opening in the abdomen that allows stool to exit the body. Then doctors repair the anorectal malformation with one or more operations when the baby is older.

Doctors may recommend regular follow-up care and additional treatments for any complications that develop after surgery or later in life.


Last Reviewed August 2019
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This content is provided as a service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), part of the National Institutes of Health. NIDDK translates and disseminates research findings to increase knowledge and understanding about health and disease among patients, health professionals, and the public. Content produced by NIDDK is carefully reviewed by NIDDK scientists and other experts.