We investigated the effect of antibiotics for the prevention of infectious complications subsequent to endscopic treatment of the colon and rectum. Thirty-three patients who underwent endoscopic polypectomies and/or hot-biopsies were divided into two groups: (A, n = 17) with and (B, n = 16) without prophylactic administration of antibiotics. The oral lavage solution method with isotonic magnesium citrate was used for bowel preparation. For group A, 250 mg of kanamycin was administered orally four times, at 30-min intervals, after the oral lavage solution of isotonic magnesium citrate was administered, and 3.2 g of clavulanic acid-ticarcillin was administered by drip infusion after the endoscopic treatment. Latent inflammatory reactions were assessed based on blood cell analysis, erythrocyte sedimentation rate, serum C-reactive protein, and serum phospholipase A2 activity before and the day after the endoscopic treatment. Postoperative platelet, white blood cell, and neutrophil counts were significantly increased in group B, while increases in these parameters were all suppressed in group A. These results suggested that bacterial infections developed subsequent to endoscopic surgery on the colon and rectum. Although we do not need to administer antibiotics to all patients, in patients at high risk of infection, such as those with leukemia or diabetes mellitus, endoscopic polypectomy or hot-biopsy of the colon and rectum should be performed with the administration of antibiotics.