Whipple's disease is a rare, chronic, and systemic infectious disease caused by the ubiquitously occurring bacterium Tropheryma whippelii. For two reasons, the disease represents a good example for documenting the input of modern molecular-based techniques into pathogenetic, diagnostic, and therapeutic concepts in clinical medicine. First, the unidentified and uncultivable causative organism has been characterized by novel molecular-genetic techniques. Second, in contrast to other chronic inflammatory disorders, clinical manifestations of T. whippelii infection seem to be based on reduced T-cell helper type 1 (TH1) activity. These findings have led to an improved pathophysiologic understanding of the disease and to new aspects in treatment strategies that are discussed in this paper.