Microbiota is defining all the microorganisms living inside and on top the human body. Looking at their numbers alone, there are more microorganisms constituting the microbiota than there are human cells in one adult human. Most of them live in the digestive tract, more precisely in the colon, where they are also the most diverse. New studies show an important connection between the microbiota and the disturbances in normal microbiota with various diseases, primarily diseases of the digestive tract. Fecal transplantation is a new therapeutic technique which transfers the healthy microbiota from the processed fecal material of a healthy donor inside a patient with dysbiosis with the aim of achieving a normal microbiota once again in the patient. There are many different techniques for fecal transplantation – oral capsules, ND/NJ tubes, gastroscopy, colonoscopy and retention enema. Today, fecal transplantation is mostly used in treating recurrent C. difficle infections (rCDI), which occurs because of a dysbiosis as a consequence of antibiotic use, primarily the use of clindamycin. Fecal transplantation became standard therapy in treatment of this disease with many treatment protocols being developed. Infalmmatory bowel disease and irritable bowel syndrome are the other gastrointestinal diseases for which research about using fecal transplantation in treatment is mostly being performed. The results of these studies are promising, and although many more bigger studies concerning the success of this therapy, defining side effects and complications and the best algorithm for it’s use, need to be performed, it looks as though in the future fecal transplantation is going to be used even more as an excellent treatment option.