Earthworms are able to protect themselves against invading pathogens due to efficient innate defense mechanisms. Currently, two types of antimicrobial factors including lysozyme-like molecule and factors with hemolytic activity, as well as a pattern recognition protein named coelomic cytolytic factor (CCF) have been identified in Eisenia foetida earthworms. However, the modulations of these defense molecules during in vivo immune response have not been addressed. In this study, we investigated the effect of experimental challenge with live Gram-negative and Gram-positive bacteria and with beta-1,3-glucan on the expression of CCF and the hemolytic factor fetidin. In parallel, we followed levels of hemolytic activity and lysozyme-like activity in the coelomic fluid of challenged earthworms. We show that the biosynthesis of CCF, but not fetidin, is up-regulated upon microbial stimulation. Parenteral administration of bacteria or microbial polysaccharides in earthworms results, in the coelomic fluid, in augmented level of CCF, increased lysozyme-like activity and decreased hemolytic activity. The decreased hemolytic activity of the coelomic fluid reflects the increase of the whole protein content in the absence of synthesis of hemolytic proteins.