To date the diagnosis of Whipple's disease is based mainly on the histopathological analysis of duodenal biopsies since Tropheryma whippelii cannot be cultured in vitro. We investigated the possibility to diagnose Whipple's disease by detection of bacterial DNA in faces. Nested polymerase chain reaction with amplification of part of the 16S rRNA gene of this bacterium in DNA extracted from faeces of a patient with Whipple's disease was performed. Sequencing of the polymerase chain reaction product revealed the sequence of Tropheryma whippelii. We conclude that Whipple's disease will be able to be diagnosed non-invasively by DNA analysis from the faeces as soon as more specific sequences of this bacteria are known.