We report simultaneous infections with Clostridium difficile and methicillin-resistant Staphylococcus aureus (MRSA) in a patient with discrete colonic pseudomembranes typical of C. difficile infection, as well as confluent, loosely adherent pseudomembranes in the small bowel. Identification of MRSA in the small bowel pseudomembrane by polymerase chain reaction supports S. aureus as an enteric pathogen.