A wide variety of signaling pathways regulate immune and stress response in invertebrates and vertebrates. The fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans are extensively utilized model organisms for studies of such signaling pathways in invertebrates. Intriguingly, major signaling pathways in immune response in Drosophila and C. elegans, as represented by the Toll and Imd pathways and the DBL-1 and DAF-2/DAF-16 pathways, respectively, are different from each other. On the other hand, the mitogen-activated protein kinase (MAPK) pathways function in common in these organisms not only in immune response but also in response to various abiotic stressors such as heat shock, ultraviolet (UV) irradiation, oxidative stress and osmotic shock. Given that all of the above pathways are highly conserved and play diverse roles in vertebrates, particularly in mammals, Drosophila and C. elegans are important invertebrate models that facilitate the elucidation of evolutionarily conserved mechanisms of immune and stress response. We therefore focus on signaling pathways that regulate immune and stress response in Drosophila and C. elegans in this review.