A case of endocarditis caused by Tropheryma whippelii is reported. The 69-year-old patient was diagnosed as suffering from severe aortic regurgitation requiring aortic valve replacement, but showed no other symptoms of Whipple's disease. T. whippelii was detected in the explanted aoritc valve by broad-range PCR amplification of the 16S rDNA and subsequent sequence analysis of the product. The etiologic agent was classified as a type 2A sequence variant based on the 16S-23S intergenic spacer and the 23S rDNA (domain III) sequences. The histological examination of the aortic valve was compatible with Whipple's disease. A duodenal biopsy revealed an infection with Giardia lamblia, but T. whippelii and histological signs of Whipple's disease were not detectable.