Studying ancient infectious diseases is a challenge, as written contemporary descriptions, when available, are often imprecise and do not allow for accurate discrimination among the pathogens endemic at that time. Paleomicrobiology offers a unique access to the history of these infections by identifying precisely the causative agents. Body louse-transmitted infections are amongst the most epidemic diseases in history, especially in war and famine periods. Of these, Bartonella quintana was detected by suicide PCR in 4000-year-old human remains, thus representing the oldest evidence to date of an arthropod-transmitted infection to human beings. This species has also been detected in human specimens from the 11th to 15th, 18th and 19th centuries. In addition, Bartonella henselae, a cat- and flea-associated pathogen, was detected in cat specimens from the 13th to 18th centuries, therefore demonstrating an association of the bacterium and its reservoir for over 800 years. Therefore, pathogenic Bartonella species have been involved in several outbreaks in the past millennia and should systematically be investigated in human remains from suspected epidemics.