Innate immunity is the first line of defense against infectious microorganisms. The innate immune system relies on germ line-encoded pattern recognition receptors (PRRs) to recognize pathogen-derived substances (Janeway 1989). Activation of the innate immune system through these receptors leads to the expression of a vast array of antimicrobial effector molecules that attack microorganisms at many different levels. The innate immune system appeared early in evolution, and the basic mechanisms of pathogen recognition and activation of the response are conserved throughout much of the animal kingdom (Hoffmann et al. 1999). In contrast to innate immunity, the adaptive immune system generates antigen-specific receptors, antibodies, and T-cell receptors by somatic cell DNA rearrangement. These receptors, found only in higher eukaryotes, recognize specific pathogen-encoded proteins. Mammals have a complex immune response, which relies on communication between the innate and adaptive arms of the immune system. The innate immune response generates a costimulatory signal, which is required in combination with antigen-specific recognition to activate T-cells and the adaptive immune system. Antigen-specific recognition in the absence of costimulation can lead to anergy rather than activation (Janeway 1989). Thus, the activation of an antigen-specific response is coupled to infection through the innate immune system. Insects have a very potent innate immune response that effectively combats a broad spectrum of pathogens. For example, Drosophila can withstand, and clear, bacterial burdens that, relative to their size, would be lethal to mammals (Hoffmann and Reichhart 1997). Induction of innate immunity in both mammals and insects leads to the activation of similar effector mechanisms, such as stimulation of cell-based phagocytic activity and expression of antimicrobial peptides (Hoffmann et al. 1999). For example, Drosophila produce a wide range of potent antimicrobial peptides in response to infection by fungi or bacteria (Hoffmann and Reichhart 1997). Induction of the antimicrobial peptides is regulated at the level of transcription, and they are expressed primarily in the fat body, the insect liver analog. Recent studies have revealed striking similarities in the signaling pathways used by humans and flies to activate their innate immune responses. In both cases, infection leads to the activation of Toll-like receptors (TLRs), which in turn initiate intracellular signaling cascades that culminate in the activation of NF-B/Rel family transcription factors. In this review, we discuss recent advances in understanding the signaling pathways in mammalian and Drosophila innate immunity, with emphasis on the mechanisms by which NF-B/Rel family proteins are activated.