Aim Comparison of functional and surgical outcome of the J-pouch with the side-to-end coloanal anastomosis after preoperative radiotherapy and total mesorectal excision in rectal cancer patients. Method In a multicentre study, patients with a carcinoma of the lower two-thirds of the rectum were randomized to either a J-pouch or a side-to-end reconstruction. Primary outcome was function of the neorectum 1year after surgery. A functional outcome [COloREctal Functional Outcome (COREFO)] questionnaire, and two quality of life questionnaires (EORTC-QLQ-CR38 and SF-36) were to be completed by all participants preoperatively, and 4 and 12months postoperatively. Independent data managers recorded surgical outcome. A group size of 30 patients in each group was calculated based on a 15-point difference of the COREFO scale. Results In total, 107 patients were randomized, 55 in the J-pouch group and 52 in the side-to-end anastomosis group. The COREFO incontinence scale at 4months and the total functional outcome at 4 and 12months showed better results for the J-pouch group in comparison with the side-to-end anastomosis group. The remaining COREFO scales (frequency, social impact, stool-related aspects and bowel medication), surgical outcome (complications, reoperations, length of hospital stay, readmissions and mortality) and quality of life did not show significant differences between treatment groups. Conclusion The overall results of a coloanal J-pouch and a side-to-end anastomosis are comparable, although functional results are slightly better with a J-pouch. The side-to-end anastomosis is technically less demanding and therefore a justified alternative in sphincter-saving surgery.