Objective: To evaluate botulinum toxin treatment of hyperactive upper esophageal sphincter after first-time brainstem stroke. Design: A retrospective study. Subjects: Twelve patients with long standing dysphagia after brainstem vascular injury admitted to the rehabilitation department of a medical centre. Methods: All patients underwent clinical examination, videofluoroscopic study of swallowing and electromyography. Botulinum toxin was injected percutaneously under electromyographic guide. Outcomes were measured after two weeks and through a long follow up programme, which ranged from two to ten years. Results: A total of 75% of patients (9 of 12) had favourable outcomes. Two patients showed long lasting functional benefits after only one botulinum toxin injection, while seven patients required further treatments to maintain an adequate oral intake. In seven cases it was possible to remove percutaneous endoscopic gastrostomy. No relevant complications were observed. Conclusion: Botulinum toxin can improve severe dysphagia with elective hyperactivity of the upper esophageal sphincter in patients with or without unilateral paresis of the inferior constrictor muscle and in absence of a nuclear involvement of the IXth and Xth cranial nerves. The outcome could be unsatisfactory in the cases of oral phase involvement, bilateral lesion of the inferior constrictor muscle and when there is velopharyngeal insufficiency.