The colonic J-pouch (pouch group) functions better than the straight coloanal anastomosis (straight group) immediately after ultra-low anterior resection, but there are few studies with long-term follow-up. This randomized controlled study compared functional outcome, anal manometry, and rectal barostat assessment of these two groups over a 2-year period. Forty-two consecutive patients were recruited, of which 19 of the straight group [17 men with a mean age of 62.1 ± 2.3 (SEM) year] and 16 of the pouch group (11 men with a mean age of 61.3 ± 3.2 year) completed the study. Four died from metastases and two emigrated; there was no surgical morbidity or local recurrence. At 6 months the Pouch patients had significantly less frequent stools (32.9 ± 2.8 vs. 49 ± 1.4/week; p<0.05) and less soiling at passing flatus (38% vs. 73.7%; p<0.05). At 2 years both groups had improved with no longer any differences in stool frequency (7.3 ± 0.4 vs. 8 ± 0.2/week) and soiling at passing flatus (38% vs. 53%). Defecation problems remained minimal in both groups. Anal squeeze pressures were significantly impaired in both groups up to 2 years (p<0.05). The rectal maximum tolerable volume and compliance were not different between groups. Rectal sensory testing on the barostat phasic program showed impairment at 6 months and recovery at 2 years, suggesting that postoperative recovery of residual afferent sympathetic nerves may play a role in functional recovery. In conclusion, stool frequency and incontinence were less in the Pouch patients at 6 months; but after adaptation at 2 years the straight group patients yielded similar results. Nonetheless, this functional advantage can be given to patients with minimal added effort or complications by using the colonic J-pouch.