Purpose of review The human gastrointestinal lumen is inhabited by a wide variety of microbiota. Our understanding of the intestinal microbiota and its full consequences on gastrointestinal health is still evolving. However, it is well accepted that altered colonic flora drives the pathogenesis of many disorders and diseases as seen in antibiotic-associated diarrhea and Clostridium difficile infection. Recent works published in the area of probiotics are reviewed here. Recent findings Alterations in colonic microbiota, or dysbiosis, are now implicated in irritable bowel syndrome and inflammatory bowel diseases. Probiotics and prebiotics are evolving treatment options that are targeted at restoring nonpathogenic digestive flora. There has been great interest in the role of these therapies in treatment of many diseases including childhood diarrhea, antibiotic-associated diarrhea, Clostridium difficile infection, irritable bowel syndrome, and inflammatory bowel disease. Summary Trials of probiotics have been shown to be helpful in some of these, not in others, and more work is needed in others. We review recent work done in these areas.