Pleomorphic adenoma (PA) is the most common benign salivary gland tumor. It is biphasic and is characterized by an admixture of epithelial and spindle-shaped myoepithelial cells in a variable background stroma. Epithelial-myoepithelial carcinoma (EMC) is a malignant biphasic salivary gland tumor typically composed of clear myoepithelial cells that surround epithelial-lined ducts resembling intercalated ducts. The differential diagnosis between the two tumor may be occasionally encountered because of the shared histophatologic feature. And then, it would be more reliable to differentiate the tumors based on biological behavior such as the expression of distinct intermediate filaments such as cytokeratin, invasiveness- related molecules, and the growth factor receptor to aberrantly facilitate the tumor growth, and the growth fraction of tumors. Therefore, from the 10 cases of PA and 6 cases of EMC, we immunohistochemically examined the differential expression of the cytokine 7 and 14, matrix metalloproteinase-9, C-KIT, and Ki-67 between the two tumor. At the results, there were significant differences of CK7 expression in non-luminal cells (P = 0.000) and CK14 expression in luminal and non-luminal cells of the both tumors (P = 0.025 and P = 0.000, respectively). In the comparison of the biologic behavior, a significantly increased expression of MMP-9, C-KIT and Ki-67 was found in the cases of EMC when compared to those of PA (P = 0.043, P = 0.011, and P = 0.000, respectively). In conclusion, the differences of CK expression in luminal and non-luminal cells between PA and EMC seem to reflect the difference of the origin and the level of the maturation of the tumor cell. Increased expression of MMP-9, C-KIT, and Ki-67 in EMC may represent more aggressive biologic behavior of the tumor compared with benign salivary tumor such as PA. Our results may be helpful to understand the histiogenesis of the two tumors and the difference of biologic behavior and to differentiate them when the limited specimen was submitted. Further study of many more cases of EMC is needed to validate the usefulness of these molecules as the diagnostic aid.