Genetic analysis of the innate immune response in Drosophila has provided important insights into the mechanism of microbial sensing and the subsequent host signalling events. The two major players following immune challenge are the Toll and Immune deficiency (IMD) pathways, which are essential for fruit flies to survive infection. These pathways are homologous to the mammalian Toll-like receptor and tumour necrosis factor pathways, respectively. Moreover, microbial pattern-recognition receptors upstream of Toll and IMD, such as the peptidoglycan recognition proteins, have been isolated and studied at the structural and functional level. In the present, we will review recent data pertaining to the genetic, genomic, RNAi and infection studies that have added new complexities to the system.