This month's issue of the Archives of Pathology & Laboratory Medicine includes a unique special section on "Molecular Signatures of Lung and Pleural Tumors" that represents the proceedings of a special Joint Symposium of the European Working Groups for Molecular Pathology and Pulmonary Pathology at the 21st European Congress of Pathology in Istanbul, Turkey, in September 2007. This symposium and the subsequent special section were organized by Dr Helmut Popper of the Institute of Pathology at the Medical University of Graz, Graz, Austria, president elect of the Austrian Society of Pathologists and immediate past president of the European Working Group for Pulmonary Pathology. In this brief review, we have provided some definitions of terms and concepts used in the proceedings of the "Molecular Signatures of Lung and Pleural Tumors" special section for those readers who are not already familiar with molecular pathology. Molecular pathology may have once been a specialized component of the research laboratory or the clinical laboratory, but today molecular diagnostic and prognostic techniques are in common use within the anatomic pathology laboratory, especially in the realm of infectious organism diagnosis and cancer diagnosis. Molecular testing continues to expand as more easily obtainable archival paraffin-embedded tissue replaces fresh and frozen tissues as the source of DNA and RNA needed for molecular analysis, and as newer technologies allow for more streamlined methods of testing. This review addresses the increased application of molecular testing in lung pathology, specifically how the current state of molecular pathology may be applied to practical, everyday lung pathology diagnosis.