14-year-old white male with a past medical history of congenital bicuspid aortic valve, Streptococcus viridans endocarditis, and pulmonary valve homograft presented with culture-negative endocarditis. Molecular studies identified the causative organism as Bartonella henselae and subsequent serologic studies supported this diagnosis. This rare cause of endocarditis may be under recognized in children. Bartonella henselae endocarditis should be considered in all children with culture-negative endocarditis, and molecular studies using a polymerase chain reaction-based assay should be routinely utilized in the evaluation of all endocarditis cases that are culture negative to rapidly diagnosis this treatable cause of endocarditis.