The community of microorganisms within the human gut (or microbiota) is critical to health and functions with a level of complexity comparable to an organ system. Alterations of this ecology (or dysbiosis) has been implicated in a number of disease states, the prototypical example being Clostridium difficile infection (CDI). Fecal microbiota transplantation (FMT) has been demonstrated to durably alter the gut microbiota of the recipient and has shown efficacy in the treatment of recurrent CDI. There is hope that FMT may eventually prove beneficial for treatment of other disease associated with alterations in gut microbiota, such as inflammatory bowel disease, irritable bowel syndrome and the metabolic syndrome, to name a few. Although the basic principles that underlie the mechanisms by which FMT demonstrates therapeutic efficacy in CDI are becoming apparent, further research is needed to understand the possible role of FMT in these other conditions. Though relatively simple to perform, questions regarding both short- and long-term safety, as well as the complex and rapidly evolving regulatory landscape has limited widespread utilization. Future work will focus on establishing best practices and more robust safety data than exist currently, as well as refining FMT beyond current “whole stool” transplants to increase safety and tolerability. Encapsulated formulations, full spectrum stool-based products and defined microbial consortia are all in the immediate future.