Rare cases of culture-negative infective endocarditis are caused by Tropheryma whipplei, the uncommon bacterium of Whipple's disease. We evaluated an 80-year-old woman with valvular heart disease but without intestinal Whipple's disease. The diagnosis of aortic valve xenograft culture-negative infection with T. whipplei was established by multiple molecular assays and by electron microscopy. First, a PCR with broad-range primers identified the complete 16S ribosomal DNA of T. whipplei in bioprosthesis tissue. Novel real-time reverse transcription-PCR assays were developed to detect mRNAs encoding recently identified proteins determined from the T. whipplei genome, specifically Whipplei surface protein (TW113) and a DNA polymerase III subunit (TW727). The positive detection of mRNAs indicated the presence of metabolically active bacteria and suggested the viability of T. whipplei. The quantification of T. whipplei genome equivalents by real-time PCR indicated a high-density bacterial colonization of the valve tissue. Additionally, an ultrastructural examination revealed numerous rod-shaped bacteria consistent in size with T. whipplei in the extracellular collagen matrix of the bioprosthesis. We conclude that extracellular growth of T. whipplei can occur in the microenvironment of biological prosthetic valve tissue and that T. whipplei endocarditis can occur in the absence of intestinal Whipple's disease.