Background: Humans are parasitized by three types of lice: body, head and pubic lice. As their common names imply, each type colonizes a specific region of the body. The body louse is the only recognized disease vector. However, an increasing awareness of head lice as a vector has emerged recently whereas the status of pubic lice as a vector is not known since it has received little attention. Methods: Here, we assessed the occurrence of bacterial pathogens in 107 body lice, 33 head lice and 63 pubic lice from Marseille and Bobigny (France) using molecular methods. Results: Results show that all body lice samples belonged to the cytb Clade A whereas head lice samples belonged to Clades A and B. DNA of Bartonella quintana was detected in 7.5% of body lice samples and, for the first time to our knowledge, in 3.1% of pubic lice samples. Coxiella burnetii, which is not usually associated with transmission by louse, was detected in 3.7% of body lice samples and 3% of head lice samples. To the best of our knowledge, this is the first report of C. burnetii in Pediculus lice infesting humans in France. Acinetobacter DNA was detected in 21.5% of body lice samples, 6% of head lice samples and 9.5% of pubic lice samples. Five species were identified with A. baumannii being the most prevalent. Conclusions: Our study is the first to report the presence of B. quintana in pubic lice. This is also the first report of the presence of DNA of C. burnetii in body lice and head lice in France. Further efforts on the vectorial role of human lice are needed, most importantly the role of pubic lice as a disease vector should be further investigated.