Botulinum toxin (Botox) was introduced for the management of internal anal sphincter (IAS) achalasia after a pull-through procedure in Hirschsprung disease (HD). We conducted a prospective evaluation of the efficacy and safety of this Botox treatment.Our study group included 15 patients with HD (median age, 4.8 years; range, 1.7-7.4 years) who experienced persistent constipation after pull-through surgery. Rectal biopsy and colon study were performed before Botox injection to exclude agangliosis. Intersphincteric Botox injections (dose, 4 IU/kg) were performed at 3 sites, (3, 6, and 9 o'clock) under general anesthesia. Measured outcomes of efficacy included anorectal manometry, Wexner constipation score and the quality of life score for defecation, measured at baseline and at 2 weeks and 3 months after injection. The Holschneider incontinence score and an assessment of pain, bleeding, heating sensation, and swelling were also performed at follow-up as outcomes of safety.There was no significant change in measured outcomes with Botox treatment. Botox did decrease the number of patients who experienced abdominal distension at 3 months, compared to 2-weeks, post-injection. No major complications were identified, with only 2 cases of anal bleeding that resolved spontaneously. Local tenderness at the injection site was reported by 4 patients, recovering without treatment.The efficacy of Botox, injected into the IAS, for the treatment of achalasia is questionable on short-term follow-up. Larger studies with a longer follow-up period and the use of repeated injections are required to evaluate the evidence for this treatment.