Imperforate anus is the historical term for a range of birth defects in which the anus and rectum do not develop properly. Today, healthcare professionals prefer the more accurate and encompassing term, Anorectal Malformation (ARM), because it covers the wide spectrum of abnormalities that can occur at the lower end of the digestive tract.

To understand ARM, it helps visualize the normal anatomy. The large intestine ends in the rectum, a chamber that holds stool before it is passed out of the body through the anus. The anus is surrounded by a complex group of sphincter muscles that are essential for bowel control (continence). In an ARM, this final segment of the digestive tract has not formed correctly.

A helpful analogy is to think of the digestive tract as a long plumbing pipe that is supposed to have a specific exit at the end.

• In anorectal malformation, this pipe was not completed correctly during construction. The malformations exist on a spectrum:
  • Low Malformations: The “pipe” (the rectum) has descended through the critical pelvic floor muscles, but the final opening on the skin is either missing, in the wrong spot, or covered by a thin membrane. The prognosis for long-term bowel control is generally very good.
  • High Malformations: The “pipe” stops high up in the pelvis, well above the crucial sphincter muscles. These are more complex defects and carry a greater risk for long-term challenges with bowel control.

The Role of Fistulas

In the vast majority of ARM cases, the underdeveloped rectum does not end blindly. Instead, it forms an abnormal connection, or fistula, to another nearby structure.

• In boys, this fistula most often connects the rectum to the urinary tract, such as the bladder or the urethra.
• In girls, the fistula most commonly connects the rectum to the vagina.

This fistula is like an emergency “spillway” that allows the meconium and stool to exit the body through an incorrect channel.

In my experience, this condition is often identified right after birth, but the variation in presentation from mild to complex, means we have to individualize care from day one.

Anorectal malformation is caused by an error in early embryonic development, specifically between the 5th and 7th weeks of gestation, when the lower end of the digestive tract is supposed to separate from the urinary tract and form the rectum and anus. In ARM, this separation and development process fails to complete correctly.

In most cases, the exact reason for this developmental error is unknown. It is important for parents to understand that it is not caused by anything they did or did not do during the pregnancy.

I always explain to families that this isn’t anyone’s fault, imperforate anus is a structural issue that arises early in fetal development, often alongside other organ anomalies.

Anorectal malformations are a congenital birth defect. The condition is not contagious.

• Sporadic Occurrence: The vast majority of cases are sporadic, meaning they occur by chance in a family with no prior history of the defect.
• Genetic Component: While most cases are random, there is a clear genetic component. ARM can sometimes be associated with specific chromosomal abnormalities (such as 22q11.2 deletion syndrome) or can be part of a broader genetic syndrome.

The VACTERL Association

Anorectal malformation is frequently one component of a recognized pattern of birth defects known as the VACTERL association. This is not a single disease, but a non-random cluster of anomalies that tend to occur together. The acronym stands for:

• V – Vertebral defects (abnormally shaped bones of the spine).
• A – Anal atresia (anorectal malformation).
• C – Cardiac (heart) defects.
• T – Tracheo-Esophageal fistula (an abnormal connection between the windpipe and the esophagus).
• R – Renal (kidney) abnormalities.
• L – Limb defects (abnormalities of the arms or legs).

Because of this strong association, any baby diagnosed with an ARM must undergo a thorough evaluation to look for these other potential problems.

Parents often feel guilt or confusion, but I reassure them: this is not caused by anything they did. It’s a rare congenital condition that simply requires prompt and coordinated care.

Most cases are identified immediately after birth during the newborn’s first physical exam. However, symptoms may vary based on the type and severity of the malformation.

The hallmark signs include:

• No visible anal opening.
• An anal opening that is in the wrong location (e.g., too close to the scrotum in a boy or the vagina in a girl).
• Failure to pass meconium (the baby’s first dark, sticky stool) within the first 24 to 48 hours after birth.
• Stool passing from an abnormal location, such as out of the urethra or the vagina.
• A swollen, distended abdomen as stool and gas build up.

One red flag I always look for is a baby who hasn’t passed stool within the first day or two. If we also see a distended belly or abnormal openings, we act quickly to investigate.

Diagnosis of ARM is usually made immediately after birth.

• Physical Examination: A doctor or nurse will perform a careful examination of the baby’s perineum (the area between the genitals and the anus). The absence or misplacement of the anal opening is the key finding.
• Imaging Workup: Once an ARM is suspected, it is considered a surgical emergency, and an urgent, comprehensive workup is initiated to determine the exact anatomy and to look for associated anomalies.
  • Abdominal X-ray: An X-ray, sometimes taken while the baby is held upside down or in a cross-table position, can help a surgeon estimate how high up the rectum has terminated in the pelvis.
  • Abdominal and Renal Ultrasound: This is performed to look for any abnormalities in the kidneys and urinary tract.
  • Echocardiogram: An ultrasound of the heart is essential to screen for any congenital heart defects.
  • Spinal Ultrasound or X-ray: These are done to look for any vertebral abnormalities or problems with the spinal cord, such as a tethered cord.

Once we suspect an imperforate anus, the next step is mapping the anatomy precisely. That guides not just surgery, but also whether we need to screen for related issues in the heart or kidneys.

Surgical correction is the main treatment and depends on the type of imperforate anus. The goals of the surgery are to create an anal opening in the correct location, position the rectum within the crucial sphincter muscle complex, and close any associated fistulas. The type and timing of the surgery depend entirely on the complexity of the malformation (high vs. low). A highly specialized pediatric surgeon manages all care.

Treatment for Low Malformations

If the baby has a low malformation, a single corrective surgery, called an anoplasty, may be all that is needed. This is often done in the early days of life. The surgeon creates an opening at the proper site and gently moves the rectum into its correct position.

Staged Treatment for High Malformations

For babies with more complex, high malformations, a staged surgical approach is usually required.

1. Initial Surgery: A Colostomy. In the first days of life, the surgeon will perform a colostomy. This involves bringing an end of the large intestine (the colon) out through a small opening (a stoma) on the abdominal wall. Stool then passes out of the stoma and is collected in a special bag. This initial surgery serves two vital purposes: it relieves the intestinal obstruction, allowing the baby to pass stool, feed, and grow, and it allows the surgical team time to get detailed imaging to precisely map out the baby’s unique anatomy before the definitive repair.
2. The Definitive Repair: A “Pull-Through” Procedure. This major reconstructive surgery is typically performed when the baby is a few months old. The most common technique is the posterior sagittal anorectoplasty (PSARP). Working through an incision between the buttocks, the surgeon carefully identifies the sphincter muscle complex. The rectum is disconnected from any fistula, gently mobilized, and then “pulled through” the center of the sphincter muscles and stitched to the newly created anal opening.
3. Colostomy Closure: A few months after the pull-through surgery has healed, a final, smaller operation is performed to close the colostomy stoma and reconnect the intestine, allowing stool to begin passing through the newly constructed anus.

Long-Term Care and Outlook

It is imperative that parents understand the surgical journey is just the beginning. While surgery creates the correct anatomy, achieving bowel control is a long process that requires dedicated management.

• Bowel Management: After the colostomy is closed, the child will need to learn how to use their new anorectal pathway. Constipation is an extremely common and serious long-term problem for children with ARM, as the repaired rectum may not have normal motility or sensation. A strict bowel management program, developed with the surgical and gastroenterology teams, involving dietary modifications, laxatives, and sometimes enemas, is often required to prevent severe constipation and to help with potty training.
• Prognosis: The long-term outlook for bowel control is generally very good for children with low malformations. For children with high or more complex malformations, the potential for achieving full continence is more variable. Some children may have lifelong challenges with constipation or soiling.

Parents often worry about the word “surgery,” but I explain that outcomes are excellent with timely correction. The bigger challenge tends to be managing bowel habits and function in the long run.

A diagnosis of an anorectal malformation, or imperforate anus, is a profound shock for any new parent. It marks the beginning of a long and challenging journey of surgeries, medical procedures, and long-term management. However, it is a journey filled with hope. Thanks to remarkable advances in pediatric surgery, particularly the development of procedures like the PSARP, surgeons can now create excellent anatomical results for most children. I always tell parents, while the diagnosis can feel overwhelming, children with imperforate anus can grow up healthy and active with the right surgical care and follow-up support.

Centers for Disease Control and Prevention (CDC). (2024). Facts about Anorectal Malformations. Retrieved from https://www.cdc.gov/ncbddd/birthdefects/anorectal-malformations.html

National Institutes of Health, Genetic and Rare Diseases Information Center (GARD). (2021). Anorectal malformation. Retrieved from https://rarediseases.info.nih.gov/diseases/5806/anorectal-malformation

Cincinnati Children’s Hospital Medical Center. (n.d.). Anorectal Malformation (Imperforate Anus). Retrieved from https://www.cincinnatichildrens.org/health/a/anorectal-malformation