The fruit fly, Drosophila melanogaster, is an extremely useful model to study innate immunity mechanisms. A fundamental understanding of these mechanisms as they relate to various pathogens has come to light over the past 30 years. The discovery of Toll-like receptors and their recognition of shared molecules (pathogen-associated molecular patterns or PAMPs) among pathogenic bacteria were the first detailed set of receptors to be described that act in innate immunity. The immune deficiency pathway (Imd) described in D. melanogaster functions in a very similar way to the Toll pathway in recognizing PAMPs primarily from Gram-negative bacteria. The discovery of small interfering RNAs (RNAi) provided a means by which antiviral immunity was accomplished in invertebrates. Another related pathway, the JAK/STAT pathway, functions in a similar manner to the interferon pathways described in vertebrates, also providing antiviral defense. Recently, autophagy was also shown to function as a protective pathway against virus infection in D. melanogaster. At least three of these pathways (Imd, JAK/STAT, and RNAi) show signal integration in response to viral infection, demonstrating a coordinated immune response against viral infection. The number of pathways and the integration of them reflect the diversity of pathogens to which innate immune mechanisms must be able to respond. The viral pathogens that infect invertebrates have developed countermeasures to some of these pathways, in particular to RNAi. The evolutionary arms race of pathogen vs. host is ever ongoing.