Chapter 25 – Ileal Pouch Anal Anastomosis


The development of the ileal pouch anal anastomosis (IPAA) has led to significant improvements in the quality of life for patients after proctocolectomy. The complex anatomy of the pouch requires a systematic examination of the different IPAA components at pouchoscopy and sampling of different histological zones, i.e. pre-pouch, pouch, rectal cuff, and anal mucosa. The main roles of the pathologist are to corroborate a clinical diagnosis of pouchitis, to identify secondary causes of inflammation when present, to be aware of the differential diagnosis, and to exclude histologically identifiable complications such as CMV infection, dysplasia and malignancy. Assessment can be difficult for several reasons, e.g. the anatomical location of a biopsy is not always obvious, adaptive changes may occur that lead to alterations in mucosal morphology, and Crohn’s-like changes may occur as a consequence of pouchitis and may cause diagnostic confusion.

Chapter 25 Ileal Pouch Anal Anastomosis

Shaun V. Walsh and Roger M. Feakins


The development of the ileal pouch anal anastomosis (IPAA) more than 40 years ago by Parks and Nicholls1 led to significant improvements in the quality of life for patients who had undergone proctocolectomy (i.e. resection of both colon and rectum). The IPAA procedure avoids the need for a long-term ileostomy. As a result of subsequent changes in surgical techniques that aimed to improve anal function, most IPAAs now include a double stapled anastomosis.2 This procedure necessitates the retention of 15–20 mm of lower rectal wall, known as the ‘rectal cuff’ (or, less precisely, the ‘columnar cuff’) between the anal transition zone distally and the ileal pouch proximally (Figure 25.1).

Figure 25.1 Diagram of ileal pouch anal anastomosis (IPAA).

The complex anatomy of the pouch requires a systematic examination of the different IPAA components at pouchoscopy. The endoscopist should then sample the different histological zones precisely, i.e. pre-pouch, pouch (sometimes from different sites separately, e.g. proximal and distal), rectal cuff, and anal mucosa, and should identify their site of origin clearly when submitting them to the pathology laboratory (Practice Points 25.1).3

Practice Points 25.1 Types of Biopsy from an Ileal Pouch Anal Anastomosis

  • Pre-pouch ileum

  • Pouch

    • May be from different sites within the pouch, e.g. proximal and distal

  • Rectal cuff

  • Anus

IPAA construction after proctocolectomy is more appropriate in some settings than in others. The most common indication is ulcerative colitis (UC), followed by familial adenomatous polyposis (FAP). Less common indications include indeterminate colitis, juvenile polyposis, and necrotising enterocolitis. Patients with Crohn’s disease very rarely undergo IPAA because there is a high risk of failure. Consideration of the procedure for Crohn’s disease requires, as a minimum, the absence of small bowel and anal disease (Practice Points 25.2).

Practice Points 25.2 Indications for ileal Pouch Anal Anastomosis Following Proctocolectomy

  • Ulcerative colitis

    • By far the most common

  • Familial adenomatous polyposis

  • ‘Indeterminate’ colitis

  • Hamartomatous polyposis

  • Necrotising enterocolitis

  • Rarely, Crohn’s disease

    • Usually a contraindication

    • Must have no small bowel disease or anal disease

Several different pathological processes may affect the IPAA. However, the clinical presentations and endoscopic appearances of these various diseases of the pouch may be similar. Broad categories of IPAA pathology include surgical mishap/mechanical problems, inflammatory/infectious processes, functional disorders, dysplasia/malignancy, and metabolic problems (Fact Sheet 25.1).4 In view of the broad differential diagnosis attributable to pouch symptomatology, the provision of adequate clinical and endoscopic information is important if the pathologist is to interpret pouch mucosal biopsies accurately and usefully.

Fact Sheet 25.1 Classification of Ileal Pouch Disorders and Associated Complications

Surgical and Mechanical

  • Anastomotic leaks

  • Pelvic sepsis and abscess

  • Pouch sinuses

  • Pouch fistulae

  • Strictures

  • Afferent limb syndrome and efferent limb syndrome

  • Infertility and sexual dysfunction

  • Portal vein thrombi

  • Pouch prolapse, twisted pouch bleeding, sphincter injury or dysfunction

Inflammatory and Infectious

  • Pouchitis

  • Cuffitis

  • CD of the pouch

  • Proximal small-bowel bacterial overgrowth

  • Inflammatory polyps


  • Irritable pouch syndrome

  • Anismus

  • Pseudo-obstruction

Dysplastic and Neoplastic

  • Dysplasia or cancer of the pouch

  • Dysplasia or cancer of the anal transitional zone

  • Systemic and metabolic anemia

  • Bone loss

  • Vitamin B12 deficiency

Reproduced with permission from Shen B, Remzi FH, Lavery IC, Lashner BA, Fazio VW. Clin Gastroenterol Hepatol. 2008;6:145–58.


Pouchitis is an inflammatory condition of the IPAA. The diagnosis depends on clinical and pathological features. It is a common problem for patients with prior UC and may occur at least once in up to 50% of these patients, although the incidence varies between studies. Risk factors for pouchitis in the setting of UC may include coexistent primary sclerosing cholangitis, extraintestinal manifestations of inflammatory bowel disease (IBD), ischaemia, severe disease, and obesity, but reports are not consistent.5 The incidence of pouchitis is lower in patients with familial adenomatous polyposis than in those with UC.

Pouchitis may be classified as acute or chronic on the basis of symptom duration, or as primary/idiopathic or secondary. The latter category includes specific infections such as CMV, Clostridioides difficile, or Candida albicans.6, 7 Pouchitis may also be secondary to drugs, resins, or radiation therapy (Fact Sheet 25.2).

Fact Sheet 25.2 Pouchitis Classification

  • Acute/chronic

  • Idiopathic/secondary

Secondary Pouchitis: Possible Causes

  • CMV

  • Clostridioides difficile

  • Candida albicans

  • Drugs

  • Resins

  • Radiation therapy

Symptoms of pouchitis include frequency, urgency, and incontinence. The pathogenesis of primary pouchitis is uncertain but faecal stasis and microbiome dysbiosis within the ileal pouch are among the possible underlying causes, and most patients respond to a course of antibiotic treatment.8

The ileal pouch mucosa undergoes a series of adaptive changes that do not produce clinical symptoms. These include villous flattening, changes in epithelial mucins, and chronic inflammation in the lamina propria without acute inflammation (Figure 25.2A and B).9 The appearances may closely resemble those of large bowel mucosa, making distinction from the adjacent rectal cuff difficult unless the endoscopist identifies each specimen site clearly.

(A) Normal ileal pouch mucosa.

(B) Adaptive changes of the ileal pouch mucosa, resulting in an appearance that may resemble colonic mucosa.

(C) Pouchitis with lamina propria inflammation and intraepithelial inflammatory cells. These changes are additional to the adaptive changes in (B).

Figure 25.2 Ileal pouch appearance.

In patients with clinical pouchitis, there are other features in addition to the adaptive villous flattening, including active inflammation in the form of acute cryptitis and crypt abscesses (Figure 25.2C). There is background acute and chronic inflammation in the lamina propria and there may be ulceration and pyloric gland metaplasia (Fact Sheet 25.3). Pyloric metaplasia and granulomas may suggest Crohn’s disease but are not specific (see later). There may be an increase in intraepithelial lymphocytes. Neuroendocrine hyperplasia may occur and is of uncertain significance.

Fact Sheet 25.3 Histology of Pouch Mucosa

Adaptive Changes

  • No clinical symptoms

  • Histology

    • Villous flattening

    • Alterations in mucins

    • Chronic inflammation in the lamina propria

    • Resemblance to large bowel mucosa


  • Symptoms

    • Frequency, urgency, incontinence

  • Histology

    • Adaptive changes, including villous blunting (as earlier)

    • Acute cryptitis

    • Crypt abscesses

    • Acute and chronic inflammation in the lamina propria

    • Ulceration

    • Pyloric metaplasia

    • Granulomas (uncommon)

    • Relatively mild crypt distortion

Several scoring systems for grading the severity of pouchitis exist.10, 11 Application of these schemes to clinical assessment is variable, but they may be very useful for research studies. The pouch disease activity index incorporates clinical, endoscopic and histopathological data in order to arrive at a diagnosis of pouchitis. Purely histological schemes also exist.

The pathology report should include a description of the mucosa and an attempt to grade the severity of chronic inflammation, acute inflammation, ulceration, and architectural changes. Table 25.1 shows a histological scheme that many pathologists use,10 either in the report or to remind themselves of the typical features of pouchitis.

Table 25.1 Scoring system for histopathological changes in IPAA pouch mucosa

Histological feature Score
Polymorph infiltration
None 0
Mild and patchy infiltrate in the surface epithelium 1
Moderate with crypt abscesses 2
Severe with crypt abscesses 3
None 0
Mild superficial 1
Moderate 2
Extensive 3
Chronic inflammatory cell infiltration:
None 0
Mild and patchy 1
Moderate 2
Severe 3
Villous atrophy:
None 0
Minor abnormality of villous architecture 1
Partial villous atrophy 2
Subtotal villous atrophy 3

Reproduced with permission from Moskowitz RL, Shepherd NA, Nicholls RJ. Int J Colorectal Dis. 1986;1:167–74.10

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Sep 2, 2020 | Posted by in GASTROENTEROLOGY | Comments Off on Chapter 25 – Ileal Pouch Anal Anastomosis

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