Deglutition, or swallowing, refers to the process of propulsion of a food bolus from the mouth into the stomach and involves the highly coordinated interplay of swallowing and breathing. At 34 weeks gestational age most neonates are capable of successful oral feeding if born at this time; however, the maturation of respiration is still in progress at this stage. Infants can experience congenital and developmental pharyngeal and/or gastrointestinal motility disorders, which might manifest clinically as gastro-oesophageal reflux (GER) symptoms, feeding difficulties and/or refusal, choking episodes and airway changes secondary to micro or overt aspiration. These problems might lead to impaired nutritional intake and failure to thrive. These gastrointestinal motility disorders are mostly classified according to the phase of swallowing in which they occur, that is, the oral preparatory, oral, pharyngeal and oesophageal phases. GER is a common phenomenon in infancy and is referred to as GERD when it causes troublesome complications. GER is predominantly caused by transient relaxation of the lower oesophageal sphincter. In oesophageal atresia, oesophageal motility disorders develop in almost all patients after surgery; however, a congenital origin of disordered motility has also been proposed. This Review highlights the prenatal development of upper gastrointestinal motility and describes the most common motility disorders that occur in early infancy.