Blood in the toilet from a BM can also mean you may have a bacterial infection that only certain antibiotics can take care of. Approx. 8 weeks ago I had mild pain in my lower right abdomen area and saw a slight bit of blood in the toilet after another bout of diarrhea.(I've had IBS for 8 years and have diarrhea typically 3-8 times a day). My MD advised I go to the hospital ER as only they had the equipment and tests to find out what was wrong. After several IVs, blood tests, a cat scan and 9 hrs in the ER, the ER Dr. diagnosed a bacterial infection in my lower colon and sent me home with the antibiotic CIPRO and a script for a 10 day supply. It made me nauseous, but it seemed to work as I've not had the bleeding again, but 4 weeks later I was diagnosed, by my regular MD, with GERD. So I'm not sure if there is any connection, but my new GI Dr. has scheduled me for an Upper Edoscopy (EDG) in late July, so we'll see what that turns up.