OBJECTIVE Functional outcome after low anterior resection with side-to-end anastomosis is comparable with that after a colonic J-pouch construction. The optimum size of the side limb has yet to be determined. This prospective randomized trial compared a 3-cm (short) and 6-cm (long) side limb. METHODS Forty-four patients with a mid or low rectal cancer undergoing low anterior resection were randomly assigned to each group. Physiologic and clinical assessments were performed preoperatively and at 3, 6, and 12 months after ileostomy closure. Defecography was performed at six months after ileostomy closure. RESULTS Twenty patients in each group completed the study. Among them, one patient with a short limb and two others with a long limb developed leakage. Sphincter function and reservoir function were similar between the groups. Bowel function or incontinence scoring was similar between the groups. The incidence of incomplete evacuation assessed by defecography in the long limb group was significantly greater than in the short limb group (13/20 long and 5/20 short, P = 0.025). One patient in the long limb group experienced fecal impaction. CONCLUSIONS The study showed similar clinical results in patients with either a short limb or a long limb but seemed to be underpowered. A long limb may be associated with fecal impaction in patients undergoing low anterior resection with side-to-end anastomosis.