I had a colonoscopy before I even knew about candida so I dont know how it can effect your treatment. I do know that they will be putting you to sleep with anesthesia but I dont know how that drug effects candida and they will ask you to fast for a day or two and clean your bowels with some crappy solution. You might want to find a more natural way of cleansing your bowels before the test as opposed to taking some pharm crap they give you. Candida probably wont show up but this test can be useful as I discovered I had polyps in my ascending colon which can develop into cancer if not attended to. I have to do a colonoscopy every 5 years now to check for them. I think you should do it but clean your bowels with enemas maybe or a colon cleanse supplement and research anesthesia.