Background: Recent advances in ileal pouchanal anastomotic (IPAA) technique include the substitution of a double stapled anastomosis for a mucosectomy and hand-sewn pouch-anal anastomosis, and the use of staples to construct a "J" shaped pouch rather than a hand-sewn "S" pouch in most cases. Method: To determine the impact these technical changes have had on pouch function, 235 IPAA patients with 15 to 155 months of follow-up (mean 70 months) were interviewed by telephone concerning pouch function and quality of life. Categorical responses were then evaluated by contingency table analysis to detect differences between mucosectomy (n = 157) and nonmucosectomy (n = 80) groups, and between J pouch (n = 50), S pouch with mucosectomy (n = 137), and S pouch nonmucosectomy (n = 30) subgroups. An index encompassing nine functional measures was used to quantify the overall impact of technique changes (optimal score 100). Results: Stool frequency for mucosectomy patients was 7.2 movements/24 hours, compared to 7.1 for nonmucosectomy patients. Elimination of a mucosectomy dramatically reduced nocturnal major incontinence (P <0.001), nocturnal minor incontinence (P <0.001), daytime minor incontinence (P = 0.03), and daytime pad use (P = 0.002). Nonmucosectomy patients had a better functional index score than had patients with an S pouch, even when only data from nonmucosectomy patients were analyzed (J = 95.5, S = 91.8, P = 0.009). Conclusions: Avoidance of a mucosectomy in the performance of an ileal pouch-anal anastomosis does not influence stool frequency but does significantly improve fecal continence and introduces no detectable morbidity associated with the retained rectal mucosa.