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The intestinal microbiota represents the microbial community that colonizes the gastrointestinal tract and constitutes the most complex ecosystem present in nature. The main intestinal microbial phyla are <i>Firmicutes</i>, <i>Bacteroidetes</i>, <i>Actinobacteria</i>, <i>Proteobacteria</i>, <i>Fusobacteria</i>, and <i>Verrucromicrobia</i>, with a clear predominance of the two phyla <i>Firmicutes</i> and <i>Bacteroidetes</i> which account for about 90% of the intestinal phyla. Intestinal microbiota alteration, or dysbiosis, has been proven to be involved in the development of various syndromes, such as non-alcoholic fatty liver disease, Crohn’s disease, and ulcerative colitis. The present review underlines the most recurrent changes in the intestinal microbiota of patients with NAFLD, Crohn’s disease, and ulcerative colitis.