Since the invention of recombinant DNA technology and the subsequent rapid development of genome editing techniques, the genes and genomes of organisms can be manipulated. Organisms whose genes or genomes have been manipulated are called transgenic or genetically modified organisms (GMOs). Probiotics, which are very important in both human and animal health and nutrition, have started to be developed for different purposes in parallel with the development of technology. Genetically modified probiotics (GMPs) are not only used as probiotics with enhanced functions but also as biological factories where various metabolites are synthesized, diagnostic tools used for diseases, targeted live drugs in treatment and vaccines, and immunomodulators in preventive medicine. Experimental studies on GMPs, which are not yet classified as drugs by the FDA (Food and Drug Administration), are promising. Studies in many fields, such as metabolic diseases, infections, cancer, autoimmune diseases, vaccinations, fighting against antibiotic resistance, and detection and elimination of targeted disease agents, reveal the potential of GMPs in a broad range of fields. In this section, GMPs, their application areas, and future perspectives will be discussed.