In this review, we first outline the basic host defense mechanisms used by Drosophila to resist and respond to invading pathogens to provide context for our discussion of how flies can be used to deconstruct key mechanisms of host-pathogen interactions. We then focus on three related topics: (1) genome-wide RNAi screens in Drosophila cell lines infected with pathogens to identify host pathways for defense or that are exploited by pathogens (e.g. bacteria, fungi, viruses); (2) classical genetic and RNAi screens conducted in intact flies to delineate host defense pathways that are active in specific tissues (e.g. the gut) or to identify important virulence factors produced by the pathogen; and (3) analysis of the function of specific pathogen virulence factors in an intact organism. The studies reviewed here highlight the speed and power of Drosophila genetics for uncovering new pathways and factors in host-pathogen interactions, as well as for characterizing unknown activities of specific virulence factors. Identification of such elements in the host-pathogen relationship should help to guide studies in vertebrate systems and contribute to defining new targets for potential therapeutic intervention.