I want to explain few investigations:
The so-called 'UPPER GI' is an contrast X-ray investigation, where a patient drinks a barium enema, and then X-ray is made to see an outline of the small intestine - which may speak for Crohn's disease but it is not a prof of it. LOWER GI is barium enema investigation of colon and terminal ileum.
During COLONOSCOPY, the entire colon and the last part of the small intestine (called terminal ileum, which is the most often affected part in Crohn's disease) is inspected and BIOPSY (a sample of tissue) is made to check it under microscope. With finding characteristic changes, diagnosis of Crohn's disease may be finally established. So, it is not enough what can be seen during colonoscopy, but what can be subsequently found in the sample of the tissue under the microscope.
If there are no other reasons, above are all intestinal investigations you need for diagnosis of Crohn's disease.
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With UPPER ENDOSCOPY, called ESOPHAGOGASTRODUODENOSCOPY, esophagus, stomach and duodenum can be checked the same ways as in colonoscopy, but the other parts of small intestine (jejunum and ileum - about 6 meters in total) can not be seen and biopsy can not be made from these parts. This upper endoscopy is not rutinely performed to confirmed Crohn's disease, but only to rule out other diseases (especially celiac disease, which often affects duodenum)
CAPSULE ENDOSCOPY is when you ingest a capsule with a camera, which records the interior of the bowel. This can again offer only images and NOT samples of tissue, so this is not for final diagnosis, and it is not necessary to perform.
You need the upper and lower scoping done. The only way the doc can really tell what is going on in the tissues is via biopsy and that can only be done by scoping. Also, the doc would need to see what areas are involved and how extensive the problem may be. That can't be accomplished in other ways. You're only short-changing yoursel in not having the tests done.
Why are you hesitating with the scopes?
The final diagnosis of Crohn's disease can be made only by biopsy - taking a sample of tissue from a colon, and especially from last part of intestine (ileum) - where the inflammation the most often is, so by colonoscopy, and not by "upper endoscopy". Tissue has to be taken and checked under microscope to see characteristic changes. Any kind of endoscopy is not enough, because the diagnosis can't be established by a naked eye or by x-ray only.
Stool tests can't tell much - bleeding can be from anything, but the doctor has to see specific inflammation in the tissue.
"Upper endoscopy" which in fact is gastroduodenoscopy would be needed to rule out celiac disease, and not for Crohn's.
You need colonoscopy with biopsy for Crohn's, and only if that would be negative, furter investigation can follow.