Body lice (Pediculus humanus humanus), obligatory human ectopasites, differ from conspecific head lice (Pediculus humanus capitas) in the choice of habitat and the capacity of disease transmission. Only body lice are known to naturally transmit a variety of human diseases, including epidemic typhus, trench fever and relapsing fever. Such differences in vectoral capacity are expected to be due to their differences in immune responses during pathogen invasion. Here, we annotated 94 immune related genes from the body louse genome and determined the differences in the transcription profiling of immune related genes between the head and body lice by qrt-PCR. In general, head louse females showed more sensitive immune responses than body louse females to Staphylococcu. aureus dermal challenge as judged by selective induction of defensin 2 in head lice. In contrast, when the 3rd nymphs were orally challenged, body lice exhibited more sensitive immune responses than head louse to Escherichia coli as judged by selective induction of defensin 1 and PGRP in body lice. These stage- and pathogen-specific differences in immune responses should provide basic insight on the vector competencies in the head and body lice.