Abstract Background Intersphincteric resection (ISR) is the ultimate sphincter-preserving operation for very low rectal cancer. The aim of this study was to assess defaecatory function after ISR in relation to the degree of resection of the internal anal sphincter. Methods Between 2001 and 2003, 35 consecutive patients with low rectal cancer had curative ISR, categorized as total, subtotal or partial resection of the internal anal sphincter. Defaecatory function was assessed in terms of frequency of bowel movements and continence. Sphincter function was evaluated by manometric study and anorectal sensation testing before surgery and 3, 6 and 12 months afterwards. Results Defaecatory function was satisfactory after ISR; 34 of 35 patients were grossly continent. The maximum resting anal canal pressure fell after all three procedures. Patients who had total ISR had reduced anal canal sensation at 3 months, but this had improved by 12 months after surgery. Conclusion These functional results suggest that ISR should be considered as an alternative to abdominoperineal resection for low rectal cancer. However, as the outcome for continence is worse after total ISR than subtotal or partial ISR, the indication for total ISR should strictly take into account the preoperative sphincter function.