The current paradigm for managing infectious diseases has targeted unique processes or enzymes within pathogens. A serious disadvantage of this pathogen-directed drug targeting strategy has been the development of microbial drug resistance and consequent resurgence of once-contained infectious diseases. A new drug discovery paradigm has therefore emerged focusing on identifying and targeting host factors essential for pathogen entry, survival, and replication. Innovative strategies combining genome-wide computational biology, genomics, proteomics, and traditional forward and reverse genetics have identified host-pathogen interactions and host functions critical for the establishment of infection. Chemogenomics and chemical genetics have allowed rapid identification of new and existing licensed drugs with antimicrobial activity. Although most host-directed drug targeting studies have focused on viral infections, they have provided a proof of concept for similar approaches to bacterial and parasite infections. Future therapies may combine conventional targeting of microbial virulence factors, together with host-directed drug therapy and augmentation of protective host factors, to efficiently eliminate the invading pathogen.