Clostridium difficile is a common pathogen, well known to medical practitioners for causing nosocomial infections. The incidence of C. difficile infection has been increasing markedly in the past two decades, with cases becoming more frequent, more severe, more refractory to the standard treatment regime and more likely to recur. Current antibiotic regimes have become less effective, and with new research on the intestinal microbiota and its effect on the nervous and immune systems and role in human health the question of possibilities of its therapeutic use and treatment for various diseases has been raised. Research has already shown remarkable results using Fecal Microbiota Transplantation in treatment for C. difficile infections, with several significant advantages over the pharmacological treatments currently used. This new and unconventional therapy shows great promise in improving treatment for C. difficile as well as multiple other gastrointestinal and non-gastrointestinal diseases, and improving human health and well-being.