The human intestinal microbiome consists of about 100 trillion (10(14)) microorganisms and has important metabolic and immunological functions. The intestinal microbiome can be influenced by antibiotics, probiotics, dietary measures, and the relatively newly established method of fecal microbiota transplantation (FMT). FMT comprises the transmission of fecal microorganisms of a healthy human donor into the gastrointestinal tract of a patient with the goal of establishing a normal microbiome in dysbiosis-associated diseases. The so far only indication for FMT that can be widely recommended is multiple recurrent Clostridium difficile infection (CDI). About 85 % of affected patients can be cured using FMT. Other possible therapeutic applications include chronic inflammatory and functional bowel diseases, nonalcoholic fatty liver disease, insulin resistance, morbid obesity, multiple sclerosis, or idiopathic thrombocytopenic purpura. These indications must be further examined in clinical trials; however, it has already been shown that the very good therapeutic success of FMT in patients with recurrent CDI cannot be readily transferred to other indications. Knowledge about the optimal donor, the best dosage, and the most appropriate route of administration for successful FMT is still incomplete. Essential is careful donor selection through accurate history, clinical examination, serology, and stool tests. The implementation of FMT in Germany is subject to the Medicines Act (Arzneimittelgesetz, AMG) with duty of disclosure and personal application by the attending physician.