Objectives Esophageal cancer development and progression is driven by the accumulation of genetic changes. In this study, we used tissue microarray to survey the expression of p53, p16 and COX-2 in esophageal cancer progression and their clinical implication. Methods We tested p53, p16 and COX-2 proteins by immunohistochemistry and tissue microarray in 86 specimens from different stages of esophageal cancer and 40 specimens from adjacent non-cancer tissue. Results The expression of p53 and COX-2 was significantly higher in tumor tissue than that in non-tumor ones. As for the expression of pl6, no significant difference was found between tumor and adjacent tissue. An obvious relation was observed among p53, p16 and COX-2 expression that esophageal carcinogenesis was highly correlated with the positive expression of p53 or COX-2, however, no reciprocal relationship to neoplastic progression was recognized with p53, p16 and COX-2. Conclusion We observed that the tissue with the positive expression of p53 or COX-2 was more likely to develop esophageal cancer. Further work will verify the hypothesis that the expression level of p53 and COX-2 in biopsy specimen is applicable to predict early outset of esophageal cancer.