Head and clothing lice from Jimma, Ethiopia were investigated for pathogenic bacteria. Genomic DNA from pools of lice was subjected to PCR analysis for Bartonella spp., Borrelia spp. Coxiella burnetii, Rickettsia spp. and Yersinia pestis. All 102 lice pools were negative for the afore mentioned pathogens, with the exception of Bartonella species found among 6 of 65 (9.2%) head lice pools and1 of 33 clothing lice pools. Identification was achieved by sequencing the ribosomal intragenic transcribed spacer region (ITS), revealing all to be Bartonella quintana. Although established as a clothing louse-borne infection, typically causing chronic bacteraemia, trench fever, bacillary angiomatosis and endocarditis, this has only been rarely reported among head lice. The higher numbers of infected head lice pools compared with clothing lice suggests their competence for maintaining this infection within Ethiopia.