Dysfunction of the upper esophageal sphincter was found in five out of 44 children with gastroesophageal reflux. Three of the five children had mental retardation associated with Silver Russell syndrome, 5p syndrome, or minimal change myopathy. The five patients had swallowing disorders, vomiting, and failure to thrive; four also had pulmonary aspiration. Esophageal manometry showed incomplete upper esophageal sphincter relaxation in two patients, upper esophageal sphincter relaxation incoordinated with pharyngeal contractions in two other patients, and both incomplete and incoordinated upper esophageal sphincter relaxation in the last patient. Intensive and successful treatment of gastroesophageal reflux did not improve swallowing or symptoms of pulmonary aspiration in four children. The fifth patient underwent cricopharyngeal myotomy, with complete resolution of respiratory and swallowing symptoms. It is suggested that a dysfunction of the upper esophageal sphincter, either primary or secondary to neuromuscular disorders, may play a role in the swallowing disorders and respiratory symptoms of pediatric patients.