The human microbiota consists of microorganisms and produces one third of the total metabolites in our body and represents one of the most heterogeneous systems. The microbiota is considered an endocrine/metabolic human organ due to the production of many compounds that affect and regulate other organ systems. The intestinal microbiota (Bacteroides, Lactobacillus, Bifidobacterium) metabolizes carbohydrates and produces short-chain fatty acids, present as salts (acetate, butyrate, propionate). These metabolites provide an important source of nutrients, and represent the regulatory factors that control the host metabolism. A large number of endocrine diseases are associated with disturbed intestinal microbiota composition and intervention with prebiotics and probiotics is proposed. Prebiotics stimulate the growth of “good intestinal” bacteria, and induce the synthesis of short-chain fatty acids. Probiotic cultures (Lactobacillus, Bifidobacterium) maintain microbiota balance and reduce the number of pathogenic bacteria. Studies have shown that probiotics reduce postprandial blood glucose level in type II diabetes mellitus, and inflammatory response in obesity and metabolic syndrome. They also increase bone mineral density in conditions like osteopenia and osteoporosis. Probiotics have strong immunomodulatory, anti-inflammatory role, and affect lipid metabolism. Nowadays, probiotics are used in the treatment and/or prevention of diseases like autoimmune thyroid disease, type II diabetes, metabolic syndrome, obesity, and osteoporosis. Probiotics also have a favorable effect on the vaginal flora. A healthy vaginal microbiota is an essential prerequisite for the preservation of fertility and maintenance of reproduction.