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The aim of this study was to evaluate the efficacy of Botulinum toxin-A (Botox) in relieving anal pain associated with anal fissure (AF) and Levator ani syndrome (LS).All patients with medically refractory AF or LS from 2005 to 2012 and treated with Botox injections were included.One hundred and three patients [66 patients (53 female) with AF and 37 patients (26 female) with LS] were evaluated. The minimum/maximum dose of Botox was 20/100 units for AF and 50/200 units for LS. Thirteen (19.7%) patients with AF and 14 (38%) patients with LS received1 Botox treatment. The time interval between injections varied from 1 to 12 months. Mean follow-up was 6.4 months for AF and 9 months for LS. Relief of anal pain was noted in 59% of AF and 43% of LS patients. Significant changes in pre- and post-op pain scores were noted in both groups. Nine out of 12 patients with failed sphincterotomy were relieved after Botox treatment. Temporary fecal incontinence was reported in 2/66 (3%) AF patients and 4/37 (10%) of LS patients. Overall, 66% patients' recommended Botox treatment and 72% were happy with the treatment as per telephone interview results.Botox relieves pain more effectively in AF than in LS. It is an effective option in medically refractory cases of LS. Higher doses of Botox are safe to use in LS; however, this needs to be evaluated. Botox injections have an overall low complication rate.