Human body and head lice have been hematophagous ectoparasites of humans for thousands of years. Although both body and head lice belong to a single species, Pediculus humanus, only body lice are known to transmit several bacterial diseases to humans. This difference in vector competence is assumed to be due to their different immune responses. Here, the immune reactions in the alimentary tract were investigated in both body and head lice following oral challenge of Escherichia coli as a model Gram-negative bacterium. In proliferation assay, head lice suppressed the growth of E. coli effectively at the early stage of infection, resulting in gradual reduction of E. coli number in alimentary tract tissues. In contrast, the number of E. coli steadily increased in alimentary tract tissues of body lice. No apparent alteration of transcription was observed following E. coli challenge in three important genes for the humoral immune responses, peptidoglycan recognition protein as a recognition gene and defensin 1 and defensin 2 as effector genes. Nevertheless, the basal transcription levels of these genes were higher in the gut tissues of body versus head lice. Considering that there is no cellular immune reaction in gut tissues, these findings suggest that the higher constitutive transcription levels of major immune genes in head lice can contribute to their rapid defense and enhanced immune capacity against intestinal bacterial infection.