We analyzed long-term morbidity and bowel function alteration after postoperative radiotherapy for rectal cancer following resection with anastomosis. Thirty-seven patients who underwent surgery with intention to cure and a minimal follow-up period of 3 years were included. These patients were divided into two groups: in the first group, 14 patients received postoperative chemo-radiotherapy, 5-fluorouracil plus folinic acid, and 45 Gy plus 5 Gy boost. In the second group, there were 23 patients regarded as controls. We designed a questionnaire about their bowel function and analyzed the morbidity detected in their follow-up. The group that was treated with postoperative chemo-radiotherapy had more daily bowel movements (p = 0.03) and night-time movements (p = 0.04); incontinence (69.2 vs. 17.4% in the control group; p = 0.002), and perianal skin irritation (p = 0.04) versus the control group. Although without meaningful differences, the group under treatment wore a pad more often, had more defecatory urgency, could distinguish worse gas from stool, and needed more frequently antidiarrheal measures. Major complications were present in 28.6% of the under-treatment group: three intestinal resections were performed due to actinic stenosis; one patient had a residual stercoral fistula; another had several occlusive crises solved with medical treatment. Postoperative chemo-radiotherapy had a high morbidity rate, which determined a significant alteration in quality of life. Accuracy in indication is therefore necessary, as well as a consideration of other alternatives for treatment, such as preoperative chemo-radiotherapy and total mesorectal excision.