Infectious endocarditis (IE) by Bartonella species is an emerging problem worldwide. We report two cases of native valve Bartonella-associated IE events, both affecting adult male patients with a history of alcohol abuse and a low socioeconomic status. Admissions were due to pancytopenia and bleeding in one case and embolic stroke in the other. Blood cultures were negative and IgG indirect immunofluorescence assays (IFA) were positive for B. henselae/B. quintana in high titers (1/16,384-1/16,384, and 1/32,768-1/16,384, respectively). Cases were classified as definitive IE events according to modified Duke criteria due to the presence of valve vegetations with at least three minor criteria. One patient required aortic mechanical valve replacement and survived, and the other died after a massive hemorrhagic transformation of his stroke. PCR amplification and sequencing of the 16S ribosomal bacterial DNA from a valve tissue sample obtained at surgery in the patient who survived, confirmed B. quintana as the etiological agent. Bartonella-associated IE is an emerging problem in Chile, present in disadvantaged populations. It should be suspected in patients with culture-negative IE. IFA does not discriminate between B. henselae and B. quintana infection, but high titers suggest IE. Complementary PCR techniques may help to elucidate the final causative agent.