To search for nasopharyngeal carcinoma (NPC) biomarkers, laser capture microdissection (LCM) was used to purify the target cells from NPC and normal nasopharyngeal epithelial tissues (NNET). Two-dimensional gel electrophoresis (2-DE) was performed to separate the total proteins of microdissected NPC and NNEC, PDQuest software was applied to analyze 2-DE images, and the differential protein spots between the two types of tissues were identified by both MALDI-TOF-MS and ESI-Q-TOF-MS. The expression of cytokeratin 8(CK8), one of the differential proteins, in the microdissected NPC and NNEC as well as 4 NPC cell lines with different differentiated degrees and/or metastatic potentials was detected by Western blot. Immunohistochemistry was also used to detect the expression of CK8 in paraffin-embedded tissues including 63 cases of primary NPC, 28 cases of NNET and 20 cases of cervical lymphonode metastasis. In the present study, 2-DE patterns of microdissected NPC and NNEC were established, and 29 differential proteins in the above two tissues were identified, of which 15 only expressed or up-regulated in NPC and 14 only expressed or up-regulated in NNET. The expression level of differential protein CK8 between the NPC and NNET was selectively confirmed, and was found to be related to the differentiation and/or metastasis of NPC cell lines. Significant down-regulation of CK8 was observed in NPC compared with NNET, and significant up-regulation of CK8 was also observed in lymphonode metastasis compared with primary NPC. The data suggest that CK8 may be related to the differentiation and lymphonode metastasis of NPC, and may serve as molecular biomarkers for metastasis and differentiation of NPC.