Toxin-antitoxin systems are modules consisting of genes that encode a stable toxin and a labile antitoxin. These systems are found in the genomes of most bacteria and archaea species. At present, eight types of toxin-antitoxin systems are distinguished. They perform a variety of functions in bacterial cells, the most important of which is adaptation to environmental stress. This review focuses on various types of toxin- antitoxin systems, their functions, and the mechanisms regulating interactions between the main components. These systems are described in detail for Bifidobacterium bifidum, Bifidobacterium longum, Lacticaseibacillus rhamnosus, and Mycobacterium tuberculosis. Furthermore, promising applications of toxin-antitoxin systems in biotechnology and infectious disease therapy are described.