OBJECTIVE It has been suggested that normal function of both anal sphincters is essential for a good functional outcome after colonic J-pouch-anal anastomosis (CPAA). However, CPAA patients may have impaired continence despite adequate sphincter function. The present study was designed to identify those factors, which contribute to the functional outcome after a handsewn CPAA. METHODS Forty patients were studied before and 1 year after pouch surgery. Faecal continence was evaluated using the Rockwood faecal incontinence severity index (RFISI). At both occasions, maximum anal resting pressure (MARP) and maximum anal squeeze pressure (MASP) were recorded. In addition, sensory perception threshold-volumes (SPT-V) and compliance were assessed using an 'infinitely' compliant polyethylene bag connected to an electronic barostat assembly. RESULTS The median RFISI score 1 year after surgery was higher than the median RFISI score before surgery (13 vs 7 (p < 0.01). The median MARP dropped significantly (p < 0.01) whereas the median MASP remained unaffected. The mean compliance, calculated at three different sensation levels, and the pouch sensory perception threshold-volumes (PSPT-V) were lower than those of the original rectum (p < 0.05). The reduction of MARP showed no correlation with the post-operative change in RFISI scores. Low PC and low PSPT-V were associated with higher RFISI scores. CONCLUSIONS Low pouch compliance and low SPT-V adversely affect functional outcome after a handsewn colonic J-pouch-anal anastomosis.