Abstract:The human intestinal flora can produce a variety of metabolites, or interact with human body to produce intestinal flora-host co-metabolites, which can impact the physiological functions of the major body systems. When the health conditions and intestinal flora change, the types and content of the metabolites will be affected accordingly, which indicate that the intestinal flora metabolites can be potential indicators for disease diagnosis. This article summarizes several common types of intestinal microbial metabolites, including carbohydrates, choline metabolites, lipids, amino acids and peptides, vitamins, bile acids, short-chain fatty acids, phenols, and benzoyl and phenyl derivatives. Furthermore, we expound their mechanisms of action in different diseases to highlight the correlations between intestinal flora, metabolites, and diseases, and to indicate that intestinal metabolites can be served as the new targets for the prevention, diagnosis, and treatment of these diseases.