In order to survive, the fruit fly Drosophila melanogaster needs to have a robust immune system to protect itself from numerous pathogenic microorganisms that are ubiquitous in its natural habitat. In two related projects, we studied the role of Rel transcription factors in mediating these immune responses. There are three Rel transcription factors, closely related to mammalian NF-KappaB: Dorsal, Dif, and Relish. They play an important role in mounting aspects of this response, including the inducible expression of antimicrobial peptides. To study the roles of these transcription factors in vivo, we used microarrays to determine the effect of null mutations in individual transcription factors on larval immune gene expression. Of the 188 genes that were significantly up-regulated in wildtype larvae upon bacterial challenge, overlapping but distinct groups of genes were affected in the Rel mutants. We also ectopically expressed Dorsal or Dif and used cDNA microarrays to determine the genes that were up-regulated in the presence of these transcription factors. Combining this data, we also identified novel genes that may be specific targets of Dif. In a related project, we observed that injection of a fungal secondary metabolite, Destruxin A reduced expression of various antimicrobial peptide genes. This reduction appeared to be mediated through suppression of the IMD pathway, through Relish. Destruxins are a class of cyclic depsipeptides produced by various fungi including the entomopathogen Metarhizium anisopliae. Though a direct relationship has been established between Destruxin production and fungal virulence, their in vivo mode of action during pathogenesis remained largely uncharacterized. To explore these effects, we looked at changes in gene expression following injection of Destruxin A into Drosophila. Microarray results revealed reduced expression of various AMPs that play a major role in the fly's humoral immune response. Flies co-injected with Destruxin A and the Gram-negative bacteria E.coli, showed increased mortality and an accompanying increase in bacterial titers. This mortality was rescued through ectopic activation of IMD pathway components upstream of Relish that are responsible for AMP induction. Together, these results suggest a novel role for Destruxin A in specific suppression of the humoral immune response in insects.