Background: Pouchitis after total rectocolectomy is among the most common complications of patients with ulcerative colitis (UC). However, its frequency is quite rare in patients with familial adenomatous polyposis (FAP). We evaluated the inflammatory and pro-apoptotic activity in endoscopically normal mucosa of the ileal pouch in patients with UC and FAP. Methods: Twenty patients (10 with UC and 10 with FAP) with "J" pouch after total proctocolectomy were studied as were 10 normal controls. Biopsies were obtained from the mucosa of the pouch of UC and FAP patients and from the normal ileum of controls. The expression levels of TNF-α, IL-1β, IL-6, IL-8 and phospho-BAD were determined by immunoblotting. Activated NFκB was evaluated by immuno-precipitation and immunoblotting for IkappaB kinase beta. Results: Patients with UC had higher levels of IL-1β, IL-6, IL-8 and TNF-α than patients with FAP. The level of TNF-α was higher in patients with UC than in patients with FAP; both patient groups had TNF-α levels higher than controls. Activation of NFκB was similar in all three groups. The expression of phospho-BAD was significantly lower in patients with FAP than in patients with UC. Conclusions: As compared with patients with FAP, patients with UC presented increased levels of some pro-inflammatory cytokines, even in the absence of clinical or endoscopic signs of pouchitis. Patients with FAP presented lower levels of pro-inflammatory proteins and of phospho-BAD. 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