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Abstract Background and purpose: To determine the effect of intrasphincteric botulinum toxin injection to treat internal anal sphincter achalasia. Materials and methods: Twenty patients (11 boys, average age 4.95± 2.47 years) with definite diagnosis of internal anal sphincter achalasia received 20 units of botulinum toxin injection in 4 points of the internal anal sphincter (totally 80 units). Then during 8 months of follow up visits, profile and response to treatment and bowel movements criteria of the patients were recorded in a questionnaire Results: All patients except one had treatment response. On 1-month follow-up, response to treatment was excellent in 35% of patients, and average in 60%. Response to treatment after 8 months follow-up was excellent in 50% and average in 40% and 10% was poor. The effect of botulinum toxin in 14 patients continued by the end of follow-up, and in 5 patients lasted between 7 to 20 weeks. The therapeutic response of these people, except one, remained moderate. Transient fecal incontinency was the only complication observed in 3 patients that was resolved after 1 to 3 weeks. Conclusion: Injection of botulinum toxin into the internal anal sphincter is an effective and safe method of treatment for achalasia, with long lasting results and few transient complications.