Purpose. We investigated intersphincteric resection with hand-sewn coloanal anastomosis, which may be an alternative to standard low anterior resection for very low rectal cancer when stapled anastomosis is technically impossible. Methods. The present study compared the clinical and functional results of 16 patients who underwent stapled colonic J-pouch low rectal anastomosis (CJLRA) with those of 15 patients who underwent intersphincteric excision and hand-sewn colonic J-pouch anal anastomosis (CJAA). Results. After a median follow-up period of 59 months, local recurrence was found in four patients from the CJAA group, three of whom subsequently underwent curative abdominoperineal resection. Defecatory function 6 and 12 months after surgery did not differ between the groups, although pads were used significantly more frequently in the CJAA group. Anorectal physiologic study before and 12 months after surgery revealed that the internal anal sphincter function was impaired to a larger extent after CJAA than after CJLRA, probably due to the partial or subtotal resection of the internal sphincter, and the anal dilatation during resection and anastomosis. Conclusion. Although the prevention of intraoperative tumor implantation and the early detection of local recurrence is of utmost importance, CJAA may be an acceptable sphincter-preserving procedure for selected patients in whom stapled anastomosis is impossible.