The innate immune system acts as an early line of defense against microbial infection in all animals. It relies on activation of multiple signaling cascades that ultimately alter the abundance of molecules in cells. In this study, we utilized RNA-Seq to investigate the immune response of C.elegans infected by the Gram-positive pathogen Bacillus thuringiensis (BT). With the help of previously published proteome data on same pathogen and worm strain, we presented a detail high throughput analysis about worm immune response at both protein and mRNA levels. As a result, we identified gene sets that reflect transcriptional and post-transcriptional mechanisms of immune response. Finally, we emphasize the important role of C-type lectin domain-containing proteins and propose that AMPKs are new regulators of the immune response to infection with BT and possibly other pathogens, which link the pathogen induced damage of cells to defence response. Overall design: mRNA profiles of wild type (WT) C.elegans exposed to either pathogenic Bacillus thuringiensis (BT) B-18247 (BT-247), non-pathogenic BT B-18407 (BT-407) or standard lab food E. coli OP50 at 6h or 12h were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.