The animals’ gastrointestinal tract is a microenvironment colonized by multiple bacterial species. Those organisms perform many important functions, inter alia the digestion aiding, enabling maturation of the colonic epithelium, participating in many metabolic changes. Keeping their stable, appropriate composition aims to protect from an excessive outgrowth of pathogenic bacteria and the development of many diseases. The gut microbiome differs significantly among species and individuals. The most common reasons for its adverse change include improper diet, disease, and certain drugs, especially antibiotics. The method ‘’faecal microbiota transplant’’ - FMT refers to a procedure of transmitting bacterial content of intestines from a healthy donor to a diseased recipient in order to help in the re-colonization of his intestines by the optimal bacteria for this environment. This results in the resolution of the disease caused by non-viable microorganisms. There are many diseases directly connected with the gut microbiota, including Clostridium difficile infection, however many studies show remarkable results in treating also many autoimmune and metabolic diseases, behavioural alterations, and neurological problems. Recent years showed directly that dysbiosis is a dangerous condition not only in conjunction with a gastrointestinal problem, but the discoveries of many years in this field may serve as proof of a great connection of all body systems and their interactions with each other and a need of implementation the holistic medical processes in treating many systemic problems. In this review, the authors summarised the available information regarding the development of a Fecal Microbiota Transplant method, evidence-based efficient methods of its application, and the newest research in this field in both human and animal medicine.