This study was undertaken to determine the incidence of and risk factors for anal incontinence after fistulotomy for intersphincteric fistula-in-ano. We also evaluated the role of anal manometry in preoperative assessment of intersphincteric fistula. A prospective, observational study was undertaken in 148 patients who underwent fistulotomy for intersphincteric fistula between January and December 2004. Functional results were assessed by standard questionnaire and anal manometry. Possible factors predicting postoperative incontinence were examined by univariate and multivariate regression analyses. The mean follow-up period was 12 months. Postoperative anal incontinence occurred in 30 patients (20.3%), i.e., soiling in 6, incontinence for flatus in 27, and incontinence for liquid stool in 4. Fistulotomy significantly decreased maximum resting pressure (85.9 +/- 20.4 to 60.2 +/- 18.4 mmHg, P < 0.0001) and length of the high pressure zone (3.92 +/- 0.69 to 3.82 +/- 0.77 cm, P = 0.035), but it did not affect voluntary contraction pressure (164.7 +/- 85.2 to 160.3 +/- 84.8 mmHg, P = 0.2792). Multivariate analysis showed low voluntary contraction pressure and multiple previous drainage surgeries to be independent risk factors for postoperative incontinence. Fistulotomy produces a satisfactory outcome in terms of eradicating sepsis and preserving function in the vast majority of patients with intersphincteric fistula with intact sphincters. However, sphincter-preserving treatment may be advocated for patients with low preoperative voluntary contraction pressure or those who have undergone multiple drainage surgeries. Preoperative anal manometry is useful in determining the proper surgical procedure.