The gut microbiota is the name given to the microbe population that colonize the digestive tract consisting of anaerobic bacteria, 90% and 10% related to other eukaryotic organisms (fungi). According to three basic well balanced states between the microbiota and the host there are determined three basic types of microbiota composition called Enterotypes which are not strictly separated. The effects that gut microbiota produces can be divided into metabolic and immunological. Polyphenols are a structural class of natural, synthetic and semi synthetic, organic chemicals characterized by the presence of large multiples of phenol structural units. They are secondary metabolites of plants in which they have multiple roles, and found in some insects and crustaceans and are known for there use as a color in the textile and food industries. Thir attributes are associated to anti-carcinogenic, anti teratogenic, anti inflammatory, antimicrobial, antiallergic and many other effects. Certain doses of some polyphenols may modify the microbiota composition by stimulating or inhibiting the growth of certain bacteria. Intestinal dysbiosis or microbial imbalance refers to disruption of the natural balance of microorganisms in the digestive tract. Specific dysbiosis are associated with obese people, patients suffering from type 2 diabetes, adolescents with high risk for type 1 diabetes, irritable bowel syndrome, inflammatory bowel disease, diarrhea associated with Clostridium difficile, colorectal carcinoma. Today nutritional components such as probiotics, prebiotics, symbiotics are more and more explored and introduced into clinical pratice. A wide range of positive effects are opening up the possibilities of lowering the risk of some chronic diseases by consuming foods rich in polyphenols. So far, most research is conducted with quercetin, resveratrol, catechins and flavones from tea, curcumin, rutin and soybeans. Probiotics are preparations of living microorganisms that have beneficial effects on the host by improving its intestinal microflora balance, strengthening the intestinal barrier and enhancing the local immune response. The mechanism of action is not yet completely clear, despite that because of their direct effect on mucosal healing probiotics are becoming an option in therapy.