Molecular biology has become an integral part of basic and clinical gastroenterology. A broad spectrum of infectious, inherited and malignant gastrointestinal diseases can now be studied by molecular methods, including polymerase chain reaction, hybridization and DNA sequence analyses. Recent progress in the molecular analysis of Whipple's disease and colorectal cancer, two major problems in clinical gastroenterology, is presented in greater detail. The implications of new molecular data for the understanding of the pathobiology of these disease entities and their clinical management are discussed.