Gastro-oesophageal reflux disease, constipation and colic are among the most common disorders in infancy and early childhood. In at least a subset of infants with these functional disorders, improvement after dietary elimination of specific food proteins has been demonstrated. Gastrointestinal food allergy should therefore be considered in the differential diagnosis of infants presenting with persistent regurgitation, constipation or irritable behaviour, particularly if conventional treatment has not been beneficial. The diagnosis of food protein-induced gastrointestinal motility disorders is hampered by the absence of specific clinical features or useful laboratory markers. Gastrointestinal biopsies before commencing a hypoallergenic diet may provide the most important diagnostic clues. Early recognition is essential for the optimal management of these patients to prevent nutritional sequelae or aversive feeding behaviours. Treatment relies on hypoallergenic formulae, as well as maternal elimination diets in breast-fed infants. Further research is required to better define the pathological mechanisms and diagnostic markers of paediatric allergic gastrointestinal motility disorders. The following article will present three instructive cases followed by discussion of the clinical presentation, diagnosis, treatment and natural history of food allergic motility disorders in infancy and early childhood.