An increasing incidence of recurrent and refractory Clostridium difficile infection (CDI) has lead to an increased need for reliable and effective therapies. Difficult-to-treat CDI has lead to the increased use of Faecal Microbiota Transplantation (FMT) in many centres worldwide. The use of FMT for C.difficile was first described in the 1950s and has been used sporadically since that time. The use of the FMT for CDI has been successfully demonstrated in a recent randomised control trial. The patient selection, method of preparation and mode of FMT delivery varies significantly, with limited use of upper gastrointestinal (GI) endoscopy delivery. Furthermore, the use of FMT for severe CDI has been limited. We report our experience with upper GI endoscopy FMT for recurrent and refractory CDI in a mixed Australian case series. Furthermore, the current alternatives, approaches and barriers to FMT for C. difficile management are explored.