Background/Aims: Preoperative chemoradiotherapy (CRT) for rectal cancer improves local control, but can also induce severe anal dysfunction after surgery. The goal of the study was to assess the relationship of the therapeutic effect of CRT with anal function and prognosis after intersphincteric resection (ISR). Methods: The subjects were 37 patients with lower rectal cancer who underwent ISR with preoperative CRT. The rectal cancer regression grade (RCRG) was quantified based on histologic features of surgical specimens. The relationships of RCRG with anal function (assessed by questionnaire) and incontinence (Wexner score) were examined at 12 months after surgery. Results: The median Wexner scores at 12 months after stoma closure in RCRG1, -2, and -3 cases were 18.0, 7.5, and 4.5, respectively, and anal function differed significantly among these groups (p = 0.001). Four cases had local recurrence, but 5-year local recurrence rates did not differ significantly among the groups. The 5-year disease-free survival rates were 88.9, 50.8, and 50.0% and the 5-year overall survival rates were 100, 77.3, and 66.7% in RCRG1, -2, and -3 cases, respectively, with no significant differences among the groups. Conclusion: Postoperative anal function is decreased when the effect of preoperative CRT is strong in patients treated with ISR.