Bacterial toxins are commonly detoxified by chemical treatment in order to use them in human vaccines. We have used site-directed mutagenesis of toxin genes to obtain bacteria that produce naturally nontoxic mutants of bacterial toxins, such as pertussis toxin (PT), cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT). Genetically detoxified PT showed a superior safety and immunogenicity in animal models, phase I and phase II clinical trials, and a superior protective efficacy in the early and late stage of a phase III efficacy trial, proving in a definitive and extensive way that genetic detoxification of bacterial toxins can, and should, replace chemical treatment. The results obtained with genetically inactivated LT and CT indicate that genetic detoxification of bacterial toxins can be used not only to produce vaccines for systemic immunization that are superior to the ones produced by conventional technologies, but suggest that these type of molecules may be the prototype molecules for the design and construction of innovative vaccines with a totally new design, such as mucosally delivered preventive and therapeutic vaccines.