Faecal microbiota transplantation (FMT) is the transferral of faeces from a healthy donor to a patient with a disease linked to disturbances in the gut microbiota. The treatment has been implemented at several hospitals in Denmark, and banks with frozen donor stool material have been established. The effect of FMT for recurrent Clostridium difficile infection is well-documented. FMT cannot be recommended for routine clinical use for inflammatory bowel disease and irritable bowel syndrome because of lack of data from clinical trials.