Molecular pathology represents a distinctive new discipline in medicine with many potential applications that have been heretofore untapped. This discipline is introducing important changes in the concepts of disease causation and in the classification of diseases. Transfer of molecular genetic technology and knowledge to the pathology laboratory is giving the pathologist new and powerful tools to diagnose, classify, and monitor disease. Methodologies such as in situ hybridization (ISH), immunohistochemistry (IHC), and the polymerase chain reaction (PCR) will continue to allow more systematic and accurate classification of human diseases. IHC and ISH allow the identification and localization of cells containing specific antigens or nucleic acid sequences. The main advantage of these methods is their ability to localize targets and define their morphologic features in various tissues, allowing correlations with histopathologic changes.