The impact of pharmacogenomics on the prevention, diagnosis, and treatment of infectious diseases is discussed. The application of pharmacogenomics to infectious diseases requires consideration of the genomes of both the pathogen and the host. The pathogen's genome may be used for antigen identification, to identify infecting organisms, and to determine antimicrobial resistance. Diagnostic tool development and vaccine design can be aided by knowing which portions of a pathogen are important antigenic determinants. The unique genetic makeup of a pathogen can facilitate its identification as an augmentation to the traditional culture. Important genes conferring resistance to antibiotics can be detected, and this information can be used to choose appropriate antibiotic therapy. The genome of the host may reveal susceptibility genes and new drug targets that may be used in the treatment of infectious diseases. Thus far, polymorphisms in genes of the host immune system have been associated with susceptibility to infections and response to treatment. Examples of these findings will be described. Pharmacogenomics has the potential to revolutionize the prevention, diagnosis, and treatment of infectious diseases.