Morphology, as confronted in the everyday practice, often correlates with specific molecular features, which have important implications not only in pathogenesis and in diagnosis but also in prognosis and therapy. Thus, it is important that the classical pathology includes a sound knowledge of molecular aspects of disease. These molecular concepts are complex and not easily understood by all engaged in the routine practice of histopathology. Thus, the aim of this review is to present a summary of most of the necessary concepts for pathologists involving molecular pathology and genetics, beginning from basic definitions and mechanisms to major abnormalities and the methodology to detect them, correlating at the same time, the specific morphologic features associated with every abnormality.