Down syndrome (DS) is a systemic disorder affecting the whole body including the gastrointestinal (GI) tract; from the oral cavity and ending with the anal canal that are involved in the food digestion absorption and excretion. These disorders could be anatomical or functional. About 10% of children born with DS have one or more forms of the structural abnormalities which may include tracheoesophageal fistula, congenital diaphragmatic hernia, small bowel obstruction, annular pancreas, and anal anomalies. Functional gastrointestinal disturbances include oral, esophageal, gastric and/or intestinal motility dysfunctions leading to feeding difficulties, prolonged feeding duration, dysphagia, gastro-oesophageal reflux disease, increased risk of aspiration, delayed gastric emptying, constipation, Hirschprung's disease and malnutrition with its effects on general health and physical compromise. These functional disturbances may be difficult to treat and may, in sequence, affect the prognosis of corrective surgeries, and hence need more cautions.