BACKGROUND AND OBJECTIVES: The correlation of biomarker expression between primary tumors and corresponding metastases has not yet been well reported in esophageal squamous cell carcinoma (ESCC). This study was to confirm whether primary ESCC tumors differ from their regional metastatic lymph nodes (RMLN) in CyclinD1, p53, E-cadherin, and vascular endothelial growth factor (VEGF) expression and determine prognostic value of their alteration. METHODS: There were 134 patients with stage T3N1-3M0 ESCC recruited for the research. Expression of CyclinD1, p53, E-cadherin, and VEGF was evaluated in primary ESCC tumors and their paired RMLN assembled on tissue microarrays by immunohistochemistry (IHC). The comparison of expression in different lesion and their correlation with prognosis was analyzed. RESULTS: E-cadherin was discordant expression in 55.2% cases and appeared to be more frequently positive in metastatic lymph nodes (P < 0.001). The VEGF expression level was significantly higher in primary tumors (P < 0.001). Combined analysis of VEGF expressions in paired lesions (P = 0.003) and its decreased expression (P = 0.006) were both predictive. CONCLUSIONS: Biomarker expression was discordant between the primary tumor and its paired lymphatic metastasis in over 25% of patient with ESCC. VEGF discordant expression was a new prognostic factor and combined analysis of expression in paired lesions was useful to predict. Analysis of protein expression only in primary tumors would be inadequate to judge prognosis. J. Surg. Oncol. 2011; 104:236–243. © 2011 Wiley-Liss, Inc.