In a 5-year retrospective study of dogs presenting to the Veterinary Medical Teaching Hospital at the University of California, Davis, there were 31 histologic diagnoses of valvular endocarditis. By polymerase chain reaction (PCR) amplification of embedded valvular tissue, Bartonella organisms were exclusively associated with 6 out of 31 cases (19%). Confirmed Bartonella cases involved the aortic valve alone (five out of six) or in combination with the mitral valve (one of six). Microscopic features of Bartonella endocarditis were compared with valves from non-Bartonella endocarditis and with valvular change unrelated to infectious agents (endocardiosis). Features of Bartonella endocarditis included a combination of fibrosis, mineralization, endothelial proliferation, and neovascularization with variable inflammation. None of these features is specific; however, the combination is distinct both from endocarditis caused by culturable bacteria and from endocardiosis. Ultrastructural analyses revealed both extracellular and intraendothelial bacteria. Clinical history, serology, and PCR are currently necessary to establish an etiologic diagnosis of Bartonella endocarditis.