BACKGROUND: DNA of Tropheryma whipplei, the etiologic agent of Whipple's disease, has recently been detected in the saliva of healthy subjects. In this pilot study we searched for the habitat of T. whipplei within the oral cavity. MATERIALS AND METHODS: Samples from different oral sites were obtained from periodontically healthy volunteers, patients with progressive periodontitis and Chinese subjects with necrotizing ulcerative gingivitis or gingivitis. Quantitative real-time PCR was performed using T. whippleispecific primers, human beta-globin-specific primers to control for tissue DNA extraction and PCR reaction and broad-range eubacterial primers to control for bacterial DNA extraction. T. whipplei specificity of multiple amplicons was confirmed by sequencing. The detection limit of the method was 10 ag of T. whipplei DNA, corresponding to one to five bacteria under reference assay conditions. RESULTS: T. whipplei was found in the oral cavity of four out of ten healthy individuals from hospital staff and in three out of nine periodontitis patients, but in none of the individuals from China. All positive samples derived from subgingival and gingival sulcus plaque containing between 10(3) and 5 x 10(5) cells ml(-1) of plaque suspension, whereas saliva, smooth surface plaque and samples from the tongue or cheeks were negative. CONCLUSION: Our results suggest that T. whipplei colonizes the human body via the oral cavity and that bacterial plaques of the gingival crevice and the gingival sulcus/pocket may serve as a natural primary habitat.