We collected 1,023 lice, representing 5 species, from rats and domestic cattle throughout 13 governorates in Egypt and tested these lice for Anaplasma marginale, Bartonella spp., Brucella spp., Borrelia recurrentis, Coxiella burnetii, Francisella tularensis, and Rickettsia spp. by PCR amplification and sequencing. Five different louse-borne bacterial agents were detected in lice from rodents or cattle, including “Bartonella rattimassiliensis”, “B. phoceensis”, and Bartonella sp. near Bartonella tribocorum, Coxiella burnetii, and Rickettsia typhi. More lice from governorates bordering the Mediterranean and Red Seas contained pathogens. Our data indicate that lice of urban and domestic animals harbor pathogenic or potentially pathogenic bacterial agents throughout Egypt.