Intestinal microbiota, which plays an important role in human health by interacting with each other or with its hosts, is afected by many endogenous and exogenous factors. Any change in the composition and functionality of the intestinal microbiota, both in number and diversity, causes disruption of intestinal functioning and paves the way for many diseases. In this regard, many antimicrobial peptides, especially bacteriocins, synthesized by lactic acid bacteria are thought to be natural resources with a high potential for the protection of the intestinal microbiota and the treatment of intestinal diseases. Both the intestinal microbiota itself and many foodborne bacteria produce bacteriocins that can inhibit pathogenic microorganisms that cause serious health problems and regulate the intestinal microbiota. This review aims to provide a comprehensive overview of the intestinal microbiota, the properties of lactic acid bacteria, their bacteriocins, and the efects of bacteriocins on the human health.