BACKGROUND: Surgical sphincterotomy for chronic anal fissure can cause fecal incontinence. This has led to the investigation of nonsurgical treatment options that avoid permanent damage to the internal anal sphincter. METHODS: We conducted a retrospective, ongoing chart review with telephone follow-up of 88 patients treated for chronic anal fissure between November 1996 and December 2002. During the first half of the study period, patients were treated with topical nitroglycerin and pneumatic dilatation. With the availability of new therapies in June 1999, subsequent patients received topical nifedipine and botulinum toxin injections (30-100 units). Lateral anal sphincterotomy was reserved for patients who failed medical treatment. RESULTS: In 98% of patients the fissure healed with conservative nonsurgical treatment. The combination of nifedipine and botulinum toxin was superior to nitroglycerin and pneumatic dilatation with respect to both healing (94% v. 71%, p < 0.05) and recurrence rate (2% v. 27%, p < 0.01). There was no statistical difference between the number of dilatations and botulinum toxin injections needed to achieve healing. Three patients who received botulinum toxin reported mild transient flatus incontinence. At an average telephone follow-up of 27 months, 92% of patients reported having no pain or only mild occasional pain with bowel movements. CONCLUSIONS: Chronic anal fissures can be simply and effectively treated medically without the risk of incontinence associated with sphincterotomy. Topical nifedipine and botulinum toxin injections are an excellent combination, associated with a low recurrence rate and minimal side effects.