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Current staging is inadequate to precisely predict clinical outcome of esophageal squamous cell carcinoma (ESCC) and determine treatment choices, which vary from operation alone to intensive multimodal regimens. The purpose of this study is to investigate the prognostic values of an immunohistochemistry-based three-protein signature model in patients with ESCC. We determined the protein expression of Annexin II, cofilin 1, ezrin, fascin, kindlin-2, moesin, MTSS1, myosin-9, profilin-1, Rac1, radixin, ROCK2, talin, tensin and villin 1 in a test cohort including 110 formalin-fixed, paraffin-embedded esophageal curative resection specimens by tissue microarrays (TMAs). A three-protein signature elicited from the protein cluster, Annexin II, kindlin-2, and myosin-9, was validated by TMAs on an independent cohort of 147 specimens. The expression of three-protein signature was highly predictive of ESCC overall survival (OS) and disease-free survival (DFS) in both generation and validation datasets. Regression analysis shows that this three-protein signature is an independent predictor for OS and DFS. Furthermore, the predictive ability of these 3 biomarkers in combination is more robust than that of each individual biomarker. This study demonstrates a clinically applicable prognostic model that accurately predicts ESCC patient survival and/or tumor recurrence, and thus could serve as a complement to current risk stratification approaches.