The incidence obesity and metabolic syndrome is increasing rapidly with Westernization of society suggesting that powerful environmental factors are playing a role. In addition to diet and other lifestyle alterations, mechanistic evidence in animal models suggest that the gut microbiota may also be playing a role. Alteration in the composition of the gut microbiota as well as their metabolites may have an important effect on host metabolic function through the activation of various mammalian receptors as well as the regulation of the immune system. Epidemiological studies also demonstrate associations between diet, the gut microbiota, and the prevalence of obesity and metabolic syndrome in human populations. Finally, early evidence in humans through fecal microbiota transplantation (FMT) suggests that the gut microbiota may have a functional role in the regulation of human metabolism in ways that may be relevant to the development of treatments for obesity and/or metabolic syndrome. However, despite this early modest level of evidence, much more research will be needed to determine the relevance of the gut microbiota to human metabolic function.