We report on the complication of gastroesophageal reflux (GER) in four patients with lower brainstem dysfunction. These patients suffered from perinatal asphyxia, cerebellar hemorrhage, or congenital dysphagia of unknown origin and showed facial nerve palsy, inspiratory stridor due to vocal cord paralysis, central sleep apnea, and dysphagia, in various combinations. Naso-intestinal tube feeding was introduced in all of the patients due to recurrent vomiting and aspiration pneumonia resulting from GER. T2-weighted magnetic resonance (MR) imaging revealed symmetrical high intensity lesions in the tegmentum of the lower pons and the medulla oblongata in two of the patients, and pontomedullary atrophy in another patient. In normal subjects, lower esophageal sphincter contraction is provoked by distension of the gastric wall, through a vago-vagal reflex. Since this reflex arc involves the solitary tract nucleus, where the swallowing center is located, the association of dysphagia and GER in the present patients is thought to result from the lesions in the tegmentum of medulla oblongata. We propose the term "dysphagia-GER complex" to describe the disturbed motility of the upper digestive tract due to lower brainstem involvement. In children with brainstem lesions, neurological assessment of GER is warranted, in addition to the examination of other signs of brainstem dysfunction, including dysphagia and respiratory disturbance.