We describe the first case of spondylodiscitis caused by Tropheryma whippelii in which this so far unculturable organism was shown to be present at the site of infection in a patient without significant gastrointestinal symptoms. The methods used included broad-range PCR amplification with universal primers complementary to constant sequences of the gene coding for 16S rRNA, direct sequencing of the amplified fragment, and comparison of the sequence determined with those deposited in sequence databases. In addition to demonstrating the presence of this organism in the affected vertebral body, we found in our patient that the specific PCR is more sensitive than histology for detecting Whipple's bacilli in bowel biopsy specimens. Because histology of small bowel biopsies from the duodenum were-in contrast to PCR from the same site-not diagnostic for Whipple's disease in our patient, we recommend PCR whenever Whipple's disease has to be excluded.