Clostridium difficile is a serious epidemiological problem and particularly dangerous microorganism causing hospital infections. Currently, the treatment of C. difficile infections is the use of metronidazole or vancomycin. However, in some patients, recurrent infection difficult to treat occurs. Fecal microbiota transplantation (FMT) is a new method used to treat the recurrent CDI. FMT consists in the infusion of the fecal suspension from a healthy donor into the gastrointestinal tract of a patient with CDI to restore the natural intestinal microflora. FMT is safe and effective treatment of recurrent CDI. FMT is extensively described around the world, but to date only two randomized studies confirming the effectiveness of FMT have been conducted. This method was also applied in the treatment of diseases such as pseudomembranous colitis, ulcerative colitis, Crohn's disease and irritable bowel syndrome. The review describes the procedure for FMT and the current state of knowledge about the effectiveness of FMT in the treatment of recurrent CDI.