The Human Microbiome Project revealed that the human microbiome comprised about 10¹⁴ bacteria. It has become clear that intestinal microbiota plays an important role not only in metabolism but also in defense against infection and differentiation of host immune cells, and systemic diseases including neuropsychiatric disorders are associated with dysbiosis. Probiotics as therapeutic methods for restoration of intestinal microbiota do not show sufficient efficacy because the number of bacteria administered is too small compared to the whole intestinal bacterial flora. To solve this problem, fecal microbiota transplantation (FMT) was developed. In clinical studies of FMT for recurrent Clostridium difficile infection, FMT treated group was overwhelmingly inhibited in relapse compared with antibiotic therapy group. Previous reports showed the efficacy of FMT for functional gastrointestinal disorders and autism. Searching for adaptive diseases of FMT is being pursued and protocols including the frequency and method of administration are being studied. Although no serious adverse event associated with FMT have been reported so far, problems such as transmission of unknown infectious diseases, complications of the whole work and invasion to patients remain. Continuous efforts are required to ensure that treatment strategies based on human wisdom develop as preemptive therapy.