The human intestinal microbiome has important metabolic and immunological functions for the host and is part of the defense against pathogens in the gastrointestinal tract. Antibiotics, probiotics, dietary measures, such as prebiotics, and the relatively newly established method of fecal microbiota transplantation (FMT, also known as fecal microbiome transfer) all influence the intestinal microbiome. The FMT procedure comprises the transmission of fecal microorganisms from a healthy donor into the gastrointestinal tract of a patient. The aim of this intervention is to restore a normal microbiome in patients with diseases associated with dysbiosis. The only indication for FMT is currently multiple recurrence of Clostridium difficile infections. Approximately 85% of affected patients can be successfully treated by FMT compared to only about 30% treated conventionally with vancomycin. Other possible therapeutic applications are chronic inflammatory and functional bowel diseases, insulin resistance and morbid obesity but these have to be evaluated further in clinical trials. Knowledge on the optimal donor, the best dosage and the most appropriate route of administration is still limited. A careful donor selection is necessary. The implementation of FMT in Germany is subject to the Medicines Act (Arzneimittelgesetz, AMG) with a duty of disclosure and personal implementation by the attending physician. By documentation in a central register long-term effects and side effects of FMT have to be evaluated.