Anorectal Malformation

Anorectal malformations occur when your baby is born with an anus or rectum that didn’t develop properly. These malformations can make it difficult or even impossible for your baby to pass stool. Treatment usually includes surgery to correct the malformation when your baby is a few days old.


What is an anorectal malformation?

An anorectal malformation is a condition in which the rectum and anus of the developing fetus don’t form properly before birth. The anus and rectum are the lower portions of the digestive tract.

Babies with anorectal malformation may have a narrowed or missing anus. Or they may be born with a layer of tissue that blocks their anus or rectum. Some babies have irregular connections between their rectum and other parts of their bodies.

It can be concerning to learn that your baby has an anorectal malformation. Without treatment, babies can develop intestinal blockages, making it difficult or impossible to pass stool (poop). But these conditions are typically treated shortly after birth with good results. Usually, a surgeon repairs an anorectal malformation when your baby is a few days old.

What does “anorectal” mean?

The word “anorectal” is a combination of the words “anus” and “rectum.” Your rectum is the last part of your large intestine, just above your anus. Your anus is the opening where stool passes.

During a bowel movement, stool passes from your rectum through your anus and out of your body. Any problems with either your anus or rectum can cause problems with bowel movements.


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How common are anorectal malformations?

Anorectal malformations are rare. They occur in about every 1 in 5,000 babies born in the United States.

Symptoms and Causes

What are the symptoms of an anorectal malformation?

A healthcare provider usually spots an anorectal malformation during a newborn exam. They may notice a narrow or missing anus. Or your baby may have an anal opening in an atypical location.

If an anorectal malformation isn’t spotted right away, babies may experience symptoms like:

  • Inability to pass stool (constipation).
  • Stool that leaks from their vagina or is visible in their urine.
  • Urine that comes from their anus.

What are the types of anorectal malformations?

There are several types of anorectal malformations, including:

  • Cloaca: The urinary tract and rectum share a single opening.
  • Fistulas: The rectum connects to other parts of your baby’s body, such as their urethra, bladder, vagina or perineum (skin between the anus and genitals), through an irregular passage.
  • Imperforate anus: The rectum and anus aren’t connected.

What causes an anorectal malformation?

Experts don’t know exactly what causes an anorectal malformation. Some think gene changes (mutations) that develop before birth may play a role.


Do children with anorectal malformations have other health problems?

Sometimes, children with anorectal malformations have other health issues. Children with anorectal malformations may also have:

Diagnosis and Tests

How is an anorectal malformation diagnosed?

Healthcare providers diagnose an anorectal malformation during a physical exam. They may use imaging tests to get a closer look or confirm your child’s diagnosis, like:

  • Barium enema tests, inserting a fluid through their rectum that coats the inside of their digestive organs so they show up more clearly on an X-ray.
  • Barium swallow tests (esophagram), swallowing a fluid that coats the inside of their digestive organs so they show up more clearly on an X-ray.
  • CT scans, using computers and X-rays to take pictures of the inside of their body.
  • MRIs, using magnets and radio waves to see inside their body.
  • Ultrasounds, using high-frequency sound waves to look at internal organs.
  • X-rays, using low doses of radiation to take pictures of the inside of their body.

Management and Treatment

How are anorectal malformations treated?

Healthcare providers usually treat anorectal malformations with surgery. They may perform a single procedure to open a narrowed passageway or remove tissue that covers your child’s anus. They may also perform a procedure called an anoplasty to reconstruct their anus.

If babies have an imperforate anus, surgeons perform a series of procedures to join the rectum and anus. These surgeries include:

  • Colostomy: The surgeon divides the large intestine and brings the two ends through openings in their stomach. Babies wear collection bags outside their body where stool and mucus pass through.
  • Anorectal repair: Surgeons typically connect the rectum and anus when your baby is a few months old. Stool continues to leave their body through the colostomy bag while they heal from surgery.
  • Colostomy closure: Babies have a procedure to remove the colostomy bags about two to three months after the second surgery. Children begin passing stool through their rectum within a few days.

Are there complications or side effects of anorectal malformation treatment?

Children who had surgery to repair an anorectal malformation may have more difficulty with toilet training than others. They may have difficulty controlling their bowel movements or they may have long-term (chronic) constipation. Adults who had anorectal malformation surgery when they were babies may also experience sexual dysfunction later in life.


How can I prevent an anorectal malformation?

There’s no way to prevent having a child with an anorectal malformation. But you can help your child live a high quality of life after anorectal malformation treatment.

If you notice your child experiencing complications of treatment — like constipation — take them to their healthcare provider right away. Your child’s provider may prescribe laxatives, dietary changes or other treatments to relieve their symptoms. They may also recommend a bowel management program if your child has trouble controlling their bowel movements.

Who is most likely to be born with an anorectal malformation?

Anorectal malformations are more common in children assigned male at birth (AMAB) than in children assigned female at birth (AFAB).

People who already had one child born with an anorectal malformation are more likely to have another child with the condition. The chances that your future child will have an anorectal malformation is about 1 in 100 if you’ve already had a child with an anorectal malformation.

Outlook / Prognosis

What is the outlook for anorectal malformations?

Most babies born with anorectal malformations are treated within the first few days of life. Many children heal well from surgery and have no complications.

Some children have long-term constipation or difficulty controlling their bowels after anorectal malformation surgery. Specialized treatment — like a bowel management program — can help.

Living With

When should I call my child’s healthcare provider?

Call your child’s healthcare provider right away if your baby:

  • Doesn’t pass any stool.
  • Has constipation.
  • Passes stool from their vagina.
  • Passes stool in their urine.
  • Passes urine from their anus.

What questions should I ask my child’s healthcare provider?

If your child has an anorectal malformation or you think they could, you may also want to ask their healthcare provider:

  • What tests do you use to diagnose an anorectal malformation?
  • Does my child need surgery to treat an anorectal malformation?
  • What are the signs of complications after anorectal malformation surgery?
  • How can I help prevent constipation in my baby?
  • How do I know if my child needs a bowel management program?

A note from Cleveland Clinic

An anorectal malformation occurs when babies are born with an anus or rectum that didn’t develop properly before birth. It can be concerning to find out your baby has been born with a congenital condition. But surgery within a few days of birth usually treats the problem. The type of surgery your child needs depends on the type and extent of the malformation. Most babies heal well after treatment.

Medically Reviewed

Last reviewed by a Cleveland Clinic medical professional on 12/15/2022.

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