Invertebrates lack an adaptive immune system and rely on innate immunity to resist pathogens. The response of Drosophila melanogaster to bacterial and fungal infections involves two signaling pathways, Toll and Imd, both of which activate members of the nuclear factor (NF)-kappaB family of transcription factors, leading to antimicrobial peptide (AMP) gene expression. In this chapter, we present the current methods used in our laboratory to monitor the activity of both signaling pathways.