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Where you are and what your insurance plan requires. Usually upper endoscopy looking at your esophagus, stomach and duodenum is done by a specialist, ie a gastroenterologist. Colonoscopy is done by a specialist, either GI or colon and rectal surgeon and some general surgeons in some areas of the country. If your ins plan requires a referral to a specialist, to obtain one beforehand.
Gastroenterologists are the most common phyician who performs colonoscopy. Some surgeons also perform them. Gastroenterologists typically do colonoscopies in the community. Family doctors will sometimes do flexible sigmoidoscopy but aren't qualified for full colonoscopy. Colorectal surgeons will also perform colonoscopy.