This chapter focuses on molecular pathology. Molecular pathology is the study of molecules in a disease state. In this context, the molecules studied are DNA, RNA and/or protein. Portions of DNA (known as genes) act as templates for the production of RNA which in turn acts as a template for the production of protein. Molecular pathology can be used to diagnose disease and/or to guide the prevention and treatment of disease. Basic concepts and terminology, methods in molecular pathology, and genetic abnormalities and molecular basis of diseases are covered in this chapter. Methods in molecular pathology includes specimen collection, sources of nucleic acid, southern blot, polymerase chain reaction, real time PCR, DNA sequencing, protein truncation test, fluorescence in situ hybridization, detecting methylation of DNA, and gene microarray technology (gene chips).