Entomopathogenic nematodes and their associated bacteria comprise together a highly pathogenic complex which is able to invade and kill insect host within two days. Both bacteria and nematodes produce a variety of factors interacting with the insect immune system and help to overcome host defences. The tripartite model (Drosophila, nematodes, bacteria) was established and used to show an immune function for candidate genes using different Drosophila mutants or RNAi lines with defects in clotting or other branches of the immune system. Microarray analysis was used to compare gene expression of Drosophila larvae infected by the entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium Photorhabdus luminescens with non-infected larvae. The role of candidate genes, selected based on genomic comparison, in response towards nematobacterial complex was further evaluated by in vivo infection assays. We demonstrated an immune function during nematode infection for known clotting enzymes and substrates, recognition molecules and eicosanoids. In conclusion, we show that the Heterorhabditis/Photorhabdus infection model is suitable to identify regulators of innate immunity in insects.