Understanding the importance of the fecal microbiota has been key in understanding the pathophysiology of some infectious diarrheas. In addition to normal protective measures of bile, gastric acid, and immune response, among others, we now know that the healthy gut flora protects us from some infectious diarrheas. Antibiotic associated diarrhea (AAD) is an excellent example, as antibiotics perturb the normal flora; the resulting diarrhea may be due to changes in short chain fatty acid metabolism. A severe form of AAD is due to Clostridium difficile, a pathogen that can cause severe diarrhea, colitis and even death. Recurrent Clostridium difficile diarrhea is a difficult clinical problem to treat successfully because one recurrence makes further recurrences more likely, probably because antibiotics are still needed to treat and thus the fecal flora remains abnormal. There is no single effective treatment but therapies include pulsed and tapered antibiotics, the probiotic Saccharomyces boulardii as an adjunct to antibiotics, and even fecal flora reconstitution. It is likely that we will learn even more in the future about the beneficial effect of our microbiota.