In this study, we report the analysis of the immune-related transcriptome from an apterygote insect, the firebrat Thermobia domestica (Zygentoma, Lepismatidae), which currently emerges as a suitable model insect for evolutionary and developmental studies. The suppression subtractive hybridization method was used for targeted screening of genes that are up-regulated in response to injected bacterial lipopolysaccharide (LPS). A subtracted cDNA library enriched in immune-inducible genes was constructed and analysis of 288 cDNAs resulted in identification of 26 novel genes in T. domestica. Among these immune-related transcripts we found homologues of genes from other insects which are involved in the regulation of signaling cascades and six novel putative antimicrobial peptides. The identified genes implicate the presence of sophisticated regulatory mechanisms in insect immune signaling and give insight into evolutionarily conserved features of insect innate immunity.