Cloacal Malformations

A cloacal malformation is a rare condition when a baby’s vagina, urinary tract and anus don’t separate from one another during fetal development. Instead of three separate openings, a female baby is born with just one opening. Surgery treats a cloacal malformation.


What is a cloacal malformation?

A cloacal malformation is a rare birth defect where an infant assigned female at birth (AFAB) is born with one opening in their perineum instead of three. Your perineum is the skin between your genitals and anus (butthole). A cloacal malformation is a type of anorectal malformation.

Early in development during pregnancy, the tissues that eventually become a baby’s intestinal, genital and urinary tracts are combined in one unit known as a “cloaca.” This unit splits into three separate units as development continues, creating an anus, vagina and urethra. Sometimes this process doesn’t work properly, and these tracts don’t separate from one another completely. When this happens, the three tracts open into one common channel, with one opening.

Treatment for a cloacal malformation involves surgery to create three separate openings. The procedures to fix the malformation typically happen within a child’s first year of life.

Types of cloacal malformations

Cloacal anomalies can differ in appearance, but all of them consist of one opening (instead of three). This one opening leads to a common area where all three tracts (rectum, urethra and vagina) join. Healthcare providers call this the common channel. The length of the common channel determines the severity of the condition and the type of treatment that the child will need. Common channels can range from 1 centimeter (cm) to 10 cm in length.

If the tracts come together at a low point, the baby has a short common channel. This means the point where the three tracts join is relatively close to the one opening. This allows waste to leave their body freely. The prognosis is usually better for children with a short channel.

In more complicated cases, the three tracts come together at a point higher up from the perineum. In these cases, the common channel is longer, which makes it more difficult for waste to pass out of the body. The channel that connects the rectum, vagina and urethra is long, and the point where the three units meet is farther away from the opening.

How common is a cloacal malformation?

Cloacal malformations are rare. They occur in about 1 in 25,000 to 1 in 50,000 newborns.


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Symptoms and Causes

What are the symptoms of a cloacal malformation?

The appearance of a cloacal malformation can vary depending on where the three tracts come together. The most common sign of a cloacal malformation is seeing one opening at birth where there should be three.

Other health problems that children with cloacal malformation may have include:

  • A clitoris that looks like a penis.
  • An abnormal appearing anus.
  • More than one vagina, uterus or cervix.
  • Kidney, ureter or other urological problems.
  • Heart or spinal cord issues.
  • Gastrointestinal (GI) problems.

What causes a cloacal malformation?

Healthcare providers don’t know why some people are born with a cloacal malformation. Researchers believe the condition happens randomly.


What are the complications of a cloacal malformation?

A cloacal malformation requires treatment shortly after birth so a newborn can get waste out of their body. Most children with cloacal malformations at birth go on to have normal urinary (pee) and bowel (poop) function. But some children may not always have full control over their pee and poop. For example, children may struggle with potty training or leak pee and poop into their school-age years.

Diagnosis and Tests

How is a cloacal malformation diagnosed?

A pregnancy care provider can sometimes diagnose a cloacal malformation on a prenatal ultrasound, most commonly around 20 weeks in pregnancy. This is usually seen as the baby having vaginal swelling from fluid buildup on the ultrasound. A magnetic resonance imaging (MRI) test during pregnancy can confirm a cloacal malformation.

After birth, a pediatrician will examine your baby and see that only one opening is present instead of three. Your baby may also have belly swelling. Your baby’s healthcare provider will order tests to get images of what’s going on inside their body.

The tests may include:

  • Ultrasound: An ultrasound can look at your child’s kidneys, bladder and spine.
  • X-rays: Your child’s provider may use special X-ray technology called fluoroscopy to see how their urinary tract is working.
  • Echocardiogram: This is a test that can diagnose heart problems.


Management and Treatment

How do you treat a cloacal malformation?

Cloacal malformation requires surgery to create three separate openings in your child’s perineum (instead of one). The goal is for your child to be able to pee and poop normally and have control over these bodily functions. The type of surgery your child has depends on the severity of their condition. It’s important to work with a pediatric urologist and pediatric surgeon who has expertise in planning and performing these types of procedures.

The first step is to make sure your baby is healthy and able to pee and poop normally. Your baby may have a colostomy shortly after birth. In a loop colostomy, a loop of intestine is brought through your child’s abdomen to the skin. It’s cut halfway through, leaving the intestine otherwise intact, but with two openings to the skin. One opening allows for poop to pass into a bag while the other allows for mucus drainage. Babies also usually need a catheter tube to help remove pee from their bladder since their bladder and kidneys are often swollen or obstructed (blocked). A surgeon may also drain your child’s vagina if fluid has accumulated in it.

As your baby ages and becomes more stable, surgeons will perform reconstructive surgery on the malformed organs. This typically happens between 6 months and 1 year of age. The reconstruction involves separating out a rectum from the common channel and then using the remaining tissues to create a vagina and a urethra. This is most easily accomplished when the common channel is short (less than 4 cm). If your child has a longer common channel, the surgeon still uses the same technique, but the procedure is more complicated.

Once this surgery is complete and your child has recovered, the surgeon will reverse your child’s colostomy so that their newly constructed rectum can function normally and begin passing poop.

Additional procedures may be necessary in the future. Your child’s healthcare provider can discuss this possibility with you.

At what age is surgery performed to treat a cloacal malformation?

The exact timeline for treatment is unique to your child’s diagnosis. Generally, surgery begins within 48 hours after birth. The first surgery, a colostomy, helps your baby poop. Your child’s surgeon will also relieve any compression in your child’s vagina. Between 6 to 12 months of age, your child will have a second surgery that creates three openings (anus, vagina and urethra) instead of one. After your child recovers from that surgery, they’ll eventually have their colostomy reversed.


Can you prevent cloacal malformation?

No, there’s nothing you can do to prevent a cloacal malformation and nothing you did to cause it. It happens randomly and is very rare.

Outlook / Prognosis

What can I expect if my child has a cloacal malformation?

The results are usually good. Babies with milder cases, where the common channel was short, have about a 90% chance of having completely normal urinary and rectal function with good control. This means they don’t leak pee or poop.

Babies who had more serious malformations or a longer common channel have about a 70% chance of having good urinary and rectal control. Most babies are eventually able to have normal bowel movements. Urinary incontinence (pee leakage) is a more frequent problem. Some children will need a catheter tube to help empty their bladder several times a day.

Most children with this condition can have an enjoyable sex life when they reach adulthood.

Living With

How can I help care for my child?

You can discuss how best to care for your child with your child’s healthcare team. The extent of the malformation and how successful the surgery is are factors for their ongoing care. Your child will need frequent follow-up appointments to make sure their body systems are functioning normally after surgery.

It’s important to be an advocate for your child’s health and let your child’s pediatrician and urologist know if you notice symptoms like urinary or bowel incontinence as they grow.

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

Finding out your child has a malformation can leave you with lots of questions. Some questions you may ask your child’s provider include:

  • How do you perform the surgeries to fix the malformation? At what age are the surgeries done?
  • Is my child going to be in pain? Are they in pain now?
  • What should I expect as my child recovers?
  • Will my child need more surgeries as they grow up?
  • Will my child have problems with their anus, urethra or vagina as they grow?
  • Will my child be able to get pregnant and have a baby safely?

Additional Common Questions

Can you get pregnant if you were born with cloacal malformation?

Pregnancy may be slightly more difficult for people with a cloacal malformation when compared to the general population. But this doesn’t mean your child can’t have children or will have fertility issues. Your child’s future healthcare provider will be able to discuss this with you once the baby is born and has had more imaging/evaluation, and they can discuss this with your child when they’re older if they wish to become pregnant.

Can you have a vaginal birth if you were born with cloacal malformation?

It’s possible for some children born with a cloacal malformation to have a vaginal delivery in the future. Oftentimes, however, a C-section is the safer option. If your child becomes pregnant when they’re older, they can discuss options for childbirth with their pregnancy care provider.

A note from Cleveland Clinic

Finding out your baby has a cloacal malformation can be shocking and leave you with lots of questions. The positive news is that surgery can fix the condition by creating separate tracts for their vagina, anus and urethra. This means people with cloacal malformations typically go on to pee, poop, menstruate and have sexual intercourse without problems. Be sure to ask your child’s healthcare provider any questions you have about the condition and how they’ll treat it. Their job is to be supportive and informative while you navigate this diagnosis and how best to care for your child.

Medically Reviewed

Last reviewed on 07/21/2023.

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