Surgery remains an important treatment option for pediatric inflammatory bowel disease (IBD)

July 29, 2025

An estimated 100,000 children in the U.S. are living with inflammatory bowel disease (IBD), according to a study published in Gastroenterology. For these children and their families, having access to a full range of treatment options is essential. Effective treatment can slow disease progression and improve quality of life in the short and long term.

IBD treatment has changed significantly over the past few decades. With the development of new medications, many pediatric patients have fewer symptoms and longer periods of remission. These advances mean that children don't require surgical management as often or as early as in the past. However, surgery still plays a key role in pediatric IBD care.

"Surgery is the only cure for ulcerative colitis," says D. Dean Potter Jr., M.D., a pediatric surgeon at Mayo Clinic in Rochester, Minnesota. "For Crohn's disease, we use surgery mainly to manage complications of the disease, although new research suggests that surgery earlier in care may be beneficial for some patients."

As part of the multidisciplinary Pediatric Inflammatory Bowel Disease Clinic at Mayo Clinic Children's, Dr. Potter meets with families early in the treatment process. "We do this knowing that most children don't need surgery right away," he says. "We discuss it as a potential treatment, so it's not a surprise if a child needs it in the future."

Ileal pouch-anal anastomosis for pediatric ulcerative colitis

The main surgical procedure for ulcerative colitis is ileal pouch-anal anastomosis (IPAA). IPAA is typically an option for children age 10 and older who don't have good disease control with medications. Sometimes, families will opt for surgery early to avoid the risks of medications.

Once an open surgery, IPAA is now usually a laparoscopic procedure performed in two or three stages, often using a single incision in children. IPAA is also one of the most complex GI operations. That means high-volume centers generally have better outcomes.

Ileal pouch-anal anastomosis (IPAA)

This laparoscopic procedure is performed in two or three stages, often with a single incision.

[This animation shows the laparoscopic procedure performed in two or three stages, often with a single incision. It is playing with no audio.]

The traditional two-stage IPAA procedure involves:

Stage 1. The surgeon removes the colon and rectum and constructs an ileal pouch (also called a J-pouch) by folding the end of the small intestine. The surgeon secures the open end to the small intestine and attaches the bottom of the J to the top of the anal canal. Then, the surgeon creates a loop ileostomy, cutting the small intestine and bringing the upper end through the abdominal wall. Waste collects in an ostomy bag while the J-pouch heals.
Stage 2. After about three months, the surgeon reconnects the cut ends of the small intestine so waste can pass as usual.

For patients who have issues with bleeding or malnutrition and are not healthy enough for a two-stage IPAA, the procedure is split into three stages. As an alternative, Dr. Potter offers a modified two-stage procedure. The first stage is a total colectomy with end ileostomy, which allows children to regain their health and improve their nutritional status. The modified second stage involves removing the remaining rectum and creating the J-pouch without a diverting loop ileostomy.

"We published a study in 2019 in the Journal of Laparoendoscopic & Advanced Surgical Techniques showing that the modified two-stage IPAA also resulted in shorter hospital stays than did the three-stage approach," explains Dr. Potter. "The patients also like the modified two-stage procedure because it avoids a third operation, and there is less time with an ileostomy."

IPAA surgery outcomes

Surgeons at Mayo Clinic started performing IPAA surgery in 1981. Using surveys of patients who underwent IPAA as children, Dr. Potter and his colleagues published a summary of long-term outcomes in the Journal of Pediatric Surgery. Overall, patients reported stable stool frequency, infrequent stool leakage and an excellent quality of life. Reports of chronic pouchitis and pouch failure were low, demonstrating the long-term durability of IPAA.

In the past, female fertility after IPAA also has been a concern. Dr. Potter has found that laparoscopic techniques have increased fertility rates to essentially 100%, although some patients need assisted reproductive technology to achieve pregnancy.

"It's great to help children with ulcerative colitis get back to their normal activities and lead full lives," says Dr. Potter.

Advances in surgery for Crohn's disease

Complications of Crohn's disease, including strictures, fistulas and abscesses, often require surgery. Dr. Potter uses laparoscopic procedures to treat these complications, enabling children to resume their lives more quickly. "With a large phlegmon, we may make a larger incision to remove the mass. But we can still do the surgery laparoscopically," he says.

Mayo Clinic researchers are evaluating new treatments. One promising approach involves the surgical implantation of stem cells to promote the healing of perianal fistulas. Technology used in a phase 1 clinical trial at Mayo Clinic involving 12 adults has been adapted for use in pediatric patients at Mayo Clinic Children's with positive initial results.

Research published in Gastroenterology in 2023 also suggests that surgery may be helpful earlier in the disease process. The traditional approach is to wait for complications to occur before recommending surgery. Based on this study, ileocecal resection may help patients with mild disease respond better to their medications.

"Although this was an adult study, physicians may want to consider referring children to a surgeon earlier to discuss it as an option," says Dr. Potter. "Our multidisciplinary group has started talking about it to families in our practice. The final verdict is still out on this option for children. But for some patients, early resection makes good sense to improve their health."