A case of culture-negative endocarditis is reported, in which the diagnosis of Cardiobacterium hominis endocarditis was made from arterio-embolic tissue removed by percutaneous transluminal embolectomy by broadrange polymerase chain reaction amplification of the 16 rRNA gene, followed by single-strand sequencing. The use of this technique to identify etiologic agents from arterio-embolic material has not been reported so far. A serologic assay employing complement fixation against a crude antigen of Cardiobacterium hominis confirmed the diagnosis of endocarditis caused by this unusual fastidious etiologic agent.