In infants with facial malformation, dysphagia is frequent and can lead to respiratory and nutritional complications whatever the phenotype. The aim of our study was to assess the severity and mechanisms of dysphagia in infants with facial malformations in order to guide therapeutic management. Forty-two newborn infants with dysphagia and recognizable malformation patterns other than isolated Pierre Robin sequence had: (1) needle electromyography (EMG) of muscles of the face, tongue, and soft palate; (2) two-channel EMG during bottle feeding; and (3) esophageal manometry (EM). The results were compared by clinical dysphagia-grading groups and by age at cessation of enteral feeding. Although micrognathia (86%) and cleft or high-arched palate (76%) were common, the key clinical finding that correlated with the likelihood of respiratory complications was glossoptosis (p<0.01). EMG signs of denervation correlated with respiratory complications (p<0.05) and the duration of enteral feeding (p<0.01). EMG during bottle feeding showed disturbed motor organization at the pharyngeal level in 27 of 37 patients. The severity of pharyngeal incoordination correlated with the duration of enteral feeding (p<0.025). All 21 patients examined by EM had dysfunction at the esophageal level. Thus, in the assessment of upper digestive tract dysfunction, our clinical grading system, EMG, and EM yield convergent information that is relevant to the management of dysphagic infants with facial malformations. Much of the information is obtainable only from EMG.