Endoscopies are generally safe. In rare circumstances, a perforation of the digestive tract may occur, which would require surgical repair. Minor bleeding may occur at the site of a polypectomy, but this typically stops on its own or may be controlled by the physician. There could be adverse reactions to the sedatives given for the procedure, but this too is rare.
Severe abdominal pain, fever or rectal bleeding needs to be reported to the physician during the post-procedure recovery period, or if they are experienced within a couple days following an endoscopic procedure.