Cloacal Malformations


What is a cloaca?

Early in the development of a female fetus, the tissue that is supposed to become the intestinal, genital, and urinary tracts are together in one unit known as a “cloaca.” These three typically separate as a pregnancy proceeds, creating the anus, the vagina, and the urethra.

In rare cases (1 in every 50,000 babies), this process does not work properly and these tracts do not separate from one another completely. A female is said to have developed a “persistent cloaca” when these three tracts open into one common cavity, with one opening from the body.

Normal Anatomy

Anatomy With Cloacal Malformation

What does a cloaca look like?

The appearance of the cloaca depends on where and how the three tracts are merged.

If they come together at a “low point,” the baby does not have a visible anus (opening where feces leave the body). However, everything else looks normal. While the tracts drain from the body via a common channel, the channel is usually short, allowing waste to leave freely and not infect any other tissue.

In more complicated cases, the three tracts come together at a “high point.” In these cases, the common channel is long. For this reason, getting waste to leave the body is more difficult. Urinary tract infections are common in these types of infants.

Patients with cloacal malformations may have other problems as well, including having a clitoris that looks like a penis. The vagina may be blocked, the anus may have an odd shape, and there may be more than one vagina and cervix. Some patients also have problems with the heart, spinal cord, or arms and legs.

Diagnosis and Tests

How are cloacal malformations diagnosed?

After a female baby is born, the doctor who examines her will see that she only has one opening instead of three. In many cases, this opening is hooded and elongated. The baby may also have abdominal swelling. The doctor will order tests to get images of what is going on inside the baby’s body.

The tests may include:

  • Ultrasound
  • Retrograde genitogram
  • Magnetic resonance imaging (MRI)
  • Echocardiogram

Management and Treatment

How are cloacal malformations treated?

Surgery is needed to treat most cloacal problems. The type of surgery the child has depends on the nature and extent of the problem. It is important to work with a pediatric urologist who has expertise in planning and performing these types of procedures.

The first priority is usually to make sure the newborn baby is healthy and able to pass feces and urine safely. If that does not happen, she may get infections or have other complications. In this case, the baby may have a surgery to create a “loop colostomy” shortly after birth. In a loop colostomy, a loop of intestine is brought through the abdomen. It is cut only half way through, leaving the intestine otherwise intact, but with two openings. The surgeon stitches it to the baby’s skin to keep it in place. Babies also usually need a catheter to help remove urine since the bladder is often swollen. The surgeon may insert a catheter and take other steps at this time, if needed, to protect the vagina or any other organ of the body that may be affected.

As the baby ages and becomes more stable, doctors are able to consider doing surgery to reconstruct the malformed organs. This typically happens between six months and one year of age. The reconstruction involves separating out a rectum from the common channel and then using the remaining tissue to create a vagina and a urethra. This is most easily accomplished when the common channel is short (less than 4 cm).

When the common channel is longer, the same approach is attempted but it will be more complicated. Some girls with this condition will have issues with urinary incontinence afterward.

The colostomy will typically be closed after three months, and the newly reconstructed areas should begin to function normally.

Outlook / Prognosis

What is the long-term outlook for a baby born with a cloacal malformation?

The results can be quite good. However, patients who had more serious problems will have varying results.

Most babies are eventually able to have normal bowel movements afterward. Urinary incontinence is a more frequent problem. Some will need to use a catheter to empty the bladder regularly.

Many patients are able to have a normal sex life when they reach adulthood. They should also be able to have children, although may need to have Cesarean sections instead of vaginal births.

Last reviewed by a Cleveland Clinic medical professional on 01/11/2017.


  • Urology Care Foundation. What are Vaginal Abnormalities: Cloacal Abnormalities? ( Accessed 1/8/2017.
  • NIH. Reconstructive Surgery in a Patient with Persistent Cloaca ( Accessed 1/8/2017.

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