BACKGROUND: Recent advances in deal pouch-anal 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 tvas 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), day-time minor incontinence (P = 0.03), and day-time 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 deal 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.