Before, During, and After J-Pouch Surgery

The ileal pouch-anal anastomosis (IPAA) procedure, commonly known as a J-Pouch procedure, is a complex surgical treatment for severe disease or injury affecting the large intestine (colon). This procedure is designed to remove the damaged tissue of the colon and allow the patient to continue to have “normal” bowel movements, meaning stool leaves the body through the anus.

During the J-Pouch procedure — or more often multiple procedures — the colon is surgically removed and the small intestine is reconstructed to allow for stool to exit the body through the anus in a controlled fashion.

Hospital doctor with digital tablet talks to male patient
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A J-Pouch By Any Other Name

This procedure, or group of procedures, has multiple names depending on the stage of surgery and the country in which it will be performed. In addition to the ileal pouch-anal anastomosis, the procedure is also known as a J-pouch, ileo-anal pouch, ileo-anal reservoir (IAR), internal pouch, restorative proctocolectomy, ileal-anal pull-through, a Kock pouch, or an ileostomy takedown.

Why the J-Pouch Surgery Is Performed

This procedure is performed for two reasons: The colon is diseased and/or damaged and must be removed, and the patient does not want an ileostomy. For many, the colon is so diseased that their life is being ruined by frequent diarrhea. It is not uncommon to hear of patients with severe inflammatory bowel disease having 25 or more bowel movements a day. These patients often are unable to leave the house for fear of having an accident due to their uncontrolled diarrhea which is often accompanied by pain, and sometimes blood in the stool.

Ileostomy Explained

An ileostomy is a surgical bypass of the large intestine that is performed by separating the end of the small intestine from the beginning of the large intestine and rerouting the end of the small intestine to the outside of the abdomen. This is done by making a small incision in the abdomen and creating an exit for stool. This incision is then covered with an appliance, a special bag with adhesives that allow it to adhere to the skin, and stool is collected in the bag.

Many people are not interested in having an ileostomy long term. While it is necessary to bypass the colon or remove the colon in some cases, patients often want an alternative to having to wear the appliance. Patients often complain that the appliance is unsightly, has an odor, interferes with sexual intimacy, irritates the skin or is generally annoying.


A colon-rectal surgeon will be the final decision-maker on whether or not a patient is a candidate for the J-Pouch procedure. That decision will be based on many factors, including the following:

  • The overall health of the patient
  • Type of problem in the large intestine
  • The severity of the problem
  • Whether or not the problem can be fixed by removal of the colon
  • Whether or not the risks of the procedure outweigh the potential benefits

The condition of the colon will not be the only factor for whether the patient is a candidate for surgery. A patient who has severe ulcerative colitis that does not respond to medication, which is the most common reason for the procedure, may not be a candidate for surgery because they have a heart condition that could make anesthesia too risky, or their diabetes is too poorly controlled.

In general, to be a candidate for the J-Pouch procedure, the patient must have severe colon disease or damage. Trauma would be a reason for damage that is treated surgically, such as a gunshot wound to the abdomen that causes significant injury to the large intestine. Medically, ulcerative colitis is the most common reason for the procedure, colon cancer is also a common reason for the colon to be removed.

Familial adenomatous polyposis, a condition that almost always leads to colon cancer, is also a common reason for J-Pouch surgery. This condition typically results in patients having colon polyps by the time they reach their mid-thirties and developing colon cancer in the decade or two that follows. The J-Pouch procedure is ideally performed prior to the diagnosis of cancer, rather than as a treatment for cancer.

Treating known Crohn’s disease — which differs from colitis in that the ulcerative lesions can appear in areas other than the colon — with J-Pouch surgery is controversial. This is because it is possible to remove the colon and create the J-Pouch only to find that the J-Pouch develops new ulcerative lesions, potentially leaving the patient worse off than when they started treatment.


In addition to the standard risks of surgery, including a reaction to anesthesia and well-known complications such as pneumonia or blood clots, there are additional risks that are specific to the ileostomy and J-Pouch procedures. These risks include:

  • Bleeding or Leaking: Both internal and external incision lines have the potential to leak or bleed after surgery.
  • Ileus: This is a complication where the muscular movements of the intestine (peristalsis) stop after anesthesia. In most cases, this resolves in the days following surgery.
  • Obstruction: This is where narrowing caused by surgery or another problem prevents the movement of food and stool through the digestive tract.

The Procedure

The J-Pouch is a small pouch formed from the end of the small intestine into a J shape where stool can wait until it is time for a bowel movement. Like the rectum, which is removed during the procedure, the muscular J-Pouch can not only store stool until it is time for a bowel movement, but the patient has some or total control over the timing of the bowel movement. In many ways, the J-Pouch is a surgically created rectum that eliminates the need for the ileostomy.

The J-Pouch procedure is typically planned to be performed in two steps, meaning two separate surgeries will be performed, often 2 to 3 months apart. Typically, the first step consists of the removal of the colon, the formation of the ileostomy, and the creation of the J-Pouch. At this point, the small intestine is separated from the large intestine, so the stool exits the body through the ileostomy site.

For the next several months the newly formed J-Pouch is allowed to heal and strengthen. Once the J-Pouch is healed and the patient is ready for additional surgery, an additional procedure is performed and stool begins to travel through the small intestine, to the J-Pouch where it is stored, then exits the body through the rectum as it did prior to these procedures.

This two surgery process is the most common way the J-Pouch procedure is performed. The procedure can also be performed as a one-step surgery, meaning the ileostomy is not performed — the colon and rectum are removed, the J-Pouch is formed and connected to the rectal stump (the small remaining portion of the rectum just inside the anus) in the same procedure.

In some cases, surgeons perform surgery in three phases, but this is less common. All steps of the procedure are performed under general anesthesia and typically result in a 3 to 7 day hospital stay, depending on the number of stages performed and the overall health of the patient.

These procedures are complex and difficult to truly understand without visual aids. For that reason, The Crohn’s and Colitis Foundation has created a video to clearly explain the J-Pouch procedure.

What to Expect After Surgery

After J-Pouch surgery has been completed, it can be many months before you reach your “new normal” for bowel movements. Normal after J-Pouch surgery doesn’t necessarily mean normal by the typical standards of the average person which are: bowel movement is controlled (not at accident), at least one every three days, formed but not hard, and non-painful. A “normal” bowel movement after J-Pouch surgery is typically the consistency of porridge or mashed potatoes.

After the recovery is complete, the average patient experiences five or six controlled bowel movements per day.

For someone who was experiencing bloody diarrhea dozens of times a day, this can seem like a wonderful improvement, but for someone who had regular bowel movements and had the procedure to prevent cancer, this may be alarming and make for a difficult adjustment.

In general, after recovery is complete and the patient has learned what foods and fluids can potentially aggravate the J-Pouch and lead to poorly controlled bowel movements, patients express satisfaction with the surgery results. Between 10 and 20 percent are dissatisfied with their outcome and elect to have an ileostomy or another procedure after having the J-Pouch procedure.

For most patients, finding the right foods to eat and avoid as well as learning what medications are helpful to decrease diarrhea and increase bowel movement control lead to an overall improvement from their previous disease state.

Potential Complications

There are many potential problems after having a J-Pouch procedure, luckily many of them are easily treated or prevented. The staff at your surgeon’s office and the enterostomal therapy nurse (nurses who specialize in the care of ostomy and other wounds) can be of significant assistance when recovering. Do not hesitate to discuss any issues with these medical professionals as they have likely seen the problem before.

Keep in mind that these issues typically improve after surgery, as the patient learns the way their body functions after surgery and recovers fully:

  • Decreased Nutrition: Frequent diarrhea can lead to fewer vitamins, minerals, and calories being absorbed by the body. Over time, patients who were malnourished prior to surgery often become better nourished once diarrhea subsides.
  • Stricture: Areas of surgical incisions, including the small intestine, J-Pouch, and anus can experience a narrowing due to scarring. This narrowing can result in small bowel obstruction, difficulty with food or stool moving through the digestive tract and difficulty with bowel movements.
  • Skin Erosion: One function of the colon is to absorb excess acid from the intestinal tract. Without the colon to perform this function, some patients experience burning at the site of their stoma or around the anus that is commonly referred to as “butt burn”. This can be prevented with a barrier ointment on the skin.
  • Pouchitis: An inflammation of the pouch, this condition can be painful and is typically treated with two medications: Flagyl and Cipro.
  • Incontinence: While the purpose of the J-Pouch is to help the patient be in control of when they move their bowels, some patients experience incontinence during their recovery. Few experience incontinence that lingers past the recovery phase.
  • Diarrhea: Technically speaking, diarrhea is six or more loose stools per day, and for some, that level of loose stools is better than their previous level of control. For others, this is worse than previous, but during the initial few weeks of recovery, diarrhea is common and expected. It is typically improved with medication such as Lomotil or Immodium along with dietary changes. Dense and starchy foods, such as potatoes and pasta, can help firm the stool. Report ongoing diarrhea to your surgeon.
  • Dehydration: Frequent bowel movements can lead to dehydration, so diarrhea should be addressed and fluid intake increased if dehydration is present. Dehydration can be best judged at home by the color of urine. Dark urine indicates an increased need for fluid, while clear and nearly colorless urine indicates adequate hydration. Report dehydration to your surgeon.
  • Low Sodium: Sodium can be lost via diarrhea, and should be replaced with electrolyte-containing fluids such as Gatorade or Pedialyte. Low sodium is typically diagnosed with lab testing, so be sure your surgeon is aware if you are found to have low sodium.
  • Pelvic Abscess: This is a pocket of infection that develops in or near the J-Pouch site and requires medical and potentially surgical treatment.
  • Sexual dysfunction: Erectile dysfunction is a known risk of the procedure for men. For women, infertility due to scarring around the ovaries is a known potential complication, as is painful intercourse.
  • Crohn’s After J-Pouch: The difference between Crohn’s and colitis is that Crohn’s disease can happen anywhere in the digestive tract while colitis is limited to the large intestine. If Crohn’s lesions only appear in the colon prior to surgery, it could logically be diagnosed as colitis, only to find that the lesions are later found in other locations after surgery. This could lead to a J-Pouch that has ulcerative lesions.
  • Small Meals: Some people with J-Pouches find they can only tolerate multiple small meals rather than three large meals per day.
  • “Normal Problems”: Standard problems faced by most individuals, such as flatulence, tend to be worse with a J-Pouch. Food that would normally cause gas may cause more gas or gas that is stinkier than it would have been prior to surgery. This is a typical outcome of the procedure, and may not resolve after the recovery is complete.
  • Need for Ostomy: In serious cases where incontinence becomes an ongoing issue, the J-Pouch isn’t healthy or non-functioning, or the patient is unsatisfied, an ileostomy is the treatment of choice.
  • Pregnancy: The pressure of the fetus in the pelvis, where the J-Pouch rests, can cause difficulty with bowel movements and continence. Both the colon-rectal surgeon and the obstetrician will play a role in helping the pregnant mother to have the best possible control during the first trimester when this problem is the most significant, and determining the best type of delivery.

A Word From Verywell

This procedure is a complex and challenging one, that is only done for patients who are either extremely ill or hoping to avoid a strong family history of colon cancer. The decision to have J-Pouch surgery is not to be taken lightly and should only be done after locating a surgeon who performs these procedures on a routine basis and after having an in-depth discussion about the risks and potential rewards of surgery.

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5 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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  2. Crohn's & Colitis Foundation. J-Pouch Surgery.

  3. American Cancer Society. What Is an Ileostomy?.

  4. Mozafar M, Shateri K, Tabatabaey A, Lotfollahzadeh S, Atqiaee K. Familial adenomatous polyposis: ileo-anal pouch versus ileo-rectal anastomosis. Gastroenterol Hepatol Bed Bench. 2014;7(4):206-10.

  5. Freeha K, Bo S. Complications Related to J-Pouch Surgery. Gastroenterol Hepatol (N Y). 2018;14(10):571-576.