Children with disorders affecting the sensory and motor functions of the esophagus will present primarily with swallowing dysfunction, dysphagia, and chest pain, and those with disorders affecting the normal function of the stomach will present with symptoms like abdominal pain, nausea, and vomiting. Recent advances in the mechanisms of disease and technology have increased our understanding of gastrointestinal physiology and that knowledge has been applied to develop new diagnostic studies and therapeutic interventions. We present an overview of the clinical presentation, diagnosis, and treatment of common primary and secondary functional and motility disorders affecting the upper gastrointestinal tract in children.