The gut microbiota is a complex and dynamic ecosystem consisting of approximately 1014 bacteria and 1 kilo of all human body mass. Idea of using gut microbiota for treatment is not new and we can consider faecal transplantation and its role in Clostridium difficile infections and inflammatory bowel diseases as a last step of its evolution. Risk factors for the infections are elderly age, chronical diseases, long-term hospital treatment, and stay in institutions for the infirm or the elderly people. More than half of all infections connected with healthcare are caused by C. difficile. Faecal transplantation is transfer of the health microbiota through infusion of liquid stool filtrate into the bowel of the receiver with the goal of normalizing the gut microbiota. The procedure of faecal transplantation consists of taking the sample from the healthy donor after which the sample is frozen and stored, then transferred to a person suffering from infection. First intervention of faecal transplantation in Croatia is performed on Clinical Hospital Centre of Rijeka Analysis of faecal transplantation application in the literature showed that on the sample of 317 patients with recurrent infections with C. difficile faecal transplantation is successful treatment method in 92 % of the cases. When treating infections, faecal microbiota is one of the most important tools of personalized approach to the patient because the natural microbiota transfer from a health donor can lead to the long-term successful treatment and improve patient’s life quality.