In this study, we have newly identified three bacteria‐induced genes from the silkworm Bombyx mori by quantitative reverse transcriptase‐polymerase chain reaction. One of these, eukaryotic initiation factor 4E‐1 (eIF4E‐1), is assumed to encode an eIF4E family, which plays a role in the initiation of translation as a mRNA cap‐binding protein. The second gene is BmFOXG1, belonging to a family of forkhead transcription factors, FOXG1. The third gene is MBF2‐related (MBF2‐R) whose product has high homology to a co‐activator protein MBF2 from B. mori. Although BmFOXG1 was up‐regulated in the fat body in response to three kinds of bacteria, Escherichia coli, Staphylococcus aureus, and Bacillus subtilis, eIF4E‐1 and MBF2‐R were up‐regulated by E. coli and B. subtilis, but not S. aureus, suggesting that bacteria possessing meso‐diaminopimelic acid‐containing peptidoglycan but not lysine‐containing peptidoglycan activate eIF4E‐1 and MBF2‐R, probably through a conserved immune deficiency pathway. We further profiled the expression of three genes in different tissues and a silkworm cell line, NIAS‐Bm‐aff3, in response to bacteria, and at different times after bacterial challenge in the fat body. © 2010 Wiley Periodicals, Inc.