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The aim of this prospective randomized trial was to compare the effectiveness and morbidity of surgical vs chemical sphincterotomy in the treatment of chronic anal fissure after a 3-year follow-up period.Eighty patients with chronic anal fissure were treated either with close lateral internal sphincterotomy (group 1) or with chemical sphincterotomy with 25 U botulinum toxin injected into the internal sphincter (group 2).Overall healing was 90% in the close sphincterotomy group and 45% in the toxin botulinum group (p0.001). There was a group of patients with clinical factors (duration of disease over 12 months and presence of a sentinel pile before treatment) associated with a higher recurrence of anal fissure. Final percentage of incontinence was 5% in the close sphincterotomy group and 0% in the botulinum toxin group (p0.05). All incontinent patients were aged more than 50 years.We recommend surgical sphincterotomy as the first therapeutic approach in patients with clinical factors of recurrence. However, we recommend the use of botulinum toxin in patients older than 50 years or with associated risk factors of incontinence, despite the higher rate of recurrence, since it avoids the greater risk of incontinence seen with surgery.