An upper endoscopy is a procedure used to visually examine your upper digestive system with a tiny camera on the end of a long, flexible tube. A specialist in diseases of the digestive system (gastroenterologist) uses endoscopy to diagnose and, sometimes, treat conditions that affect the esophagus, stomach and beginning of the small intestine (duodenum).The medical term for an upper endoscopy is esophagogastroduodenoscopy. An upper endoscopy may be done in your doctor's office, an outpatient surgery center or a hospital.