The vital roles that intestinal flora, now called microbiota, have in maintaining our health are being increasingly appreciated. Starting with birth, exposure to the outside world begins the life-long intimate association our microbiota will have with our diet and environment, and initiates determination of the post-natal structural and functional maturation of the gut. Moreover, vital interactions of the microbiota with our metabolic activities, as well as with the immunological apparatus that constitutes our major defense system against foreign antigens continues throughout life. A perturbed intestinal microbiome has been associated with an increasing number of gastrointestinal and non-gastrointestinal diseases includingClostridium difficileinfection (CDI). It has become recognized that fecal microbiota transplantation (FMT) can correct the dysbiosis that characterizes chronic CDI, and effect a seemingly safe, relatively inexpensive, and rapidly effective cure in the vast majority of patients so treated. In addition, FMT has been used to treat an array of other gastrointestinal and non-gastrointestinal disorders, although experience in these other non-CDI diseases is in its infancy. More work needs to be done with FMT to ensure its safety and optimal route of administration. There is a conceptual sea change that is developing in our view of bacteria from their role only as pathogens to that of being critical to health maintenance in a changing world. Future studies are certain to narrow the spectrum of organisms that need to be given to patients to cure disease. FMT is but the first step in this journey.