Objective of the Review: To discuss changes in intestinal microbiota in various diseases. Key Points. Microbial intestinal imbalance plays an important role in pathogenesis and/or progression of a number of diseases, namely of Clostridium difficile-associated disorders, intestinal inflammations, obesity, colorectal cancer, autistic disorders and other. Moreover, therapies involving faecal microbiota transplantation, use of pro- and prebiotics, metabiotics proved efficient in management of some of the above disorders. Conclusion. So far, some mechanisms have been explored which explain possible participation of intestinal microbiota in pathogenesis of colorectal cancer, intestine inflammation, type 2 diabetes milletus, and hepatic disorders. Still, additional information is required to allow using available facts in clinical practice. Keywords: microbiota, microbiome, faecal microbiota transplantation, probiotics.