Recent developments in high-throughput microbial genomic sequencing and other systems biology techniques have allowed novel insight into the potential contribution of the gut microbiota to health and disease. Consequently, an increasing number of disease states have been found to be characterizedby distinctive changes in the composition and functionality of the gut microbiota; however, whether such changes are cause, consequence or incidental to the disease in question remains largely uncertain. Restoration of the gut microbiota to a pre-morbid state isa novel therapeutic approachof key interest, and faecal microbiota transplantation (FMT) –the transfer of pre-screened stool from healthy donors into the gastrointestinal tract of affected patients –is gaining increasing importance in both the clinical and research settings. At present, FMT is only recommended in the treatment of recurrent Clostridioides difficile infection, although there are a large number of ongoing trials worldwide exploring other potential therapeutic indications.