The anesthesia is the wprst of it; the endoscopy itself is a short procedure and if under anesthesia, the baby will not be aware of it at all. For anyone who is older and having this done, it really is no big deal at all. One second you are getting an IV, the VERY NEXT SECOND (as far as you will be concerned), the procedure is already over. You will have no recollection of time passing, though ti will probably take about 20 minutes or so.
While we are on the subject, if you have not yet had a colonoscopy and are 50 or more years old, or if you are younger and there is a family history of a problem, PLEASE arrange to have this test done ASAP. It really is nothing with nothing, and the test itself can save lives. The prep the day before is nowhere near as awful as I always envisioned it.