Objective: To investigate the expression of epithelial membrane antigen (EMA) in tissue of papillary thyroid carcinoma (PTC) and Hashimoto’s thyroiditis and the clinical significance. Methods: The EMA protein expression in specimens of PTC tissue from 54 patients and tissue specimens of PTC adjacent Hashimoto's thyroiditis in 15 cases and metastatic lymph nodes in 12 cases, and normal thyroid tissues from 10 subjects were determined by immunohistochemical staining. The relations of EMA protein expression with the clinicopathologic features of the patients were analyzed. Results: EMA protein expression was found in the cytoplasm and cell membrane/inner surface of cell membrane. The positive expression rate of cytoplasm EMA in normal thyroid tissue, tissue of Hashimoto’s thyroiditis, PTC and lymph node metastases was 80.0%, 25.0%, 64.8%, and 35.7% respectively, and the difference had statistical significance (P<0.05). The cytoplasm EMA positive expression was significantly associated with the tumor size of the patients (P<0.05). The positive expression rate of EMA in the cell membrane/inner surface of cell membrane in normal thyroid tissue, tissue of Hashimoto’s thyroiditis, PTC and lymph node metastases was 10.0%, 100.0%, 44.4% and 64.3% respectively, and the difference had statistical significance (P<0.05); the EMA positive expression in the cell membrane/inner surface of cell membrane was irrelevant to any clinicopathologic factors of the patients (all P>0.05). Conclusion: High EMA expression in the cell membrane/inner surface of cell membrane may suggest a high possibility of transformation of Hashimoto’s thyroiditis to PTC. Decreased EMA expression in the cytoplasm can probably be used as an auxiliary index for screening of thyroid microcarcinoma.