Purpose: The purpose of this study was to prospectively compare rectal resection (RR) with colonic resection on sexual, urinary and bowel function and quality of life in both short-term and long-term. Methods: Eighty-three patients who underwent RR were compared to 53 patients who underwent a colonic resection leaving the rectum in situ (RIS). A questionnaire assessing sexual, urinary and bowel functioning with a quality of life questionnaire (SF-36) was sent to all participants preoperatively, 3 and 12 months postoperatively and approximately 8 years after the onset of the study. Results: Short-term dysfunction included diminished sexual activity in female RR patients at 3 months and significantly more erectile dysfunction in RR patients 1 year postoperatively. Long-term dysfunction included more frequent and more severe erectile dysfunction in RR patients compared to RIS patients. These short-term and long-term outcomes did not influence overall quality of life. The incidence of urinary dysfunction was comparable between both groups. Bowel functioning was significantly better in the RIS group compared to the RR group 3 months and 1 year postoperatively. Conclusions: Patients who underwent RR experienced up to 1 year postoperatively more sexual and bowel function problems than RIS patients. However, short-term and long-term dysfunction did not influence overall quality of life. Erectile dysfunction in male RR patients persisted in time, whereas other aspects of sexual, urinary and bowel function after RR and colonic resection are similar after a median follow-up of 8.5 years.