With applications of recent development of molecular techniques, endocrine pathology, as a scientific discipline, has been expanding its field to cover not only the pathologic diagnosis but also molecular mechanisms of hormone production and secretion as well as implementation for appropriate therapeutic approaches. In this review, the discussion includes molecular markers for the diagnosis of neuroendocrine (NE) tumors focusing on various proteins for the transport of secretory granules. MIB-1, proliferative indices, is particularly useful to access biologic activities of NE tumors. The specific hormone production relies on the expression of combination of transcription factors and proteolytic digestion (processing) of prohormones by specific enzymes, prohormone convertases PC1/3 and PC2. Inappropriate processing of prohormones sometimes are related to neoplastic conditions. Endocrine therapeutics have been focusing on the compensation of deficient hormones by transplanting specific hormone producing cells including embryonic stem (ES) cells. The endocrine pathology is expected to play a major role in translational medicine.