Abstract: Objective:To search for potential protein biomarkers of papillary thyroid carcinoma (PTC) and thyroid borderline lesion. Dif -ferentially expressed proteins between the two were analyzed and identified. Methods:A total of 118 cases of thyroid resection sam-ples were obtained from patients who underwent surgery at the First People's Hospital of Yunnan Province from April 2013to Febru -ary 2015. Experimental groups included 43PTCs (40classic and 3 follicular variants) and 33thyroid borderline lesions (with equivocal PTC type nuclear features and papillary structure, but without metastasis, and lacking capsular or vascular invasion;8 cases with atypi -cal adenoma), respectively. The control group included 42normal thyroid tissues adjacent to carcinoma. The total protein extracts from frozen thyroid samples of 10cases in each group were profiled with 2D electrophoresis. The differential protein spots were then revealed by PDQUEST 7. 3 software and identified by matrix-assisted laser desorption ionization time-of-fight/ time-of-fight mass spec -trometry and Swiss-Prot database search. Six differentially expressed proteins of these spots were further validated using 118 samples through immunohistochemistry. Results: A set of 24differentially expressed spots significant in discriminating between the sample groups were found, and 18proteins were identified. Immunohistochemistry revealed the following six proteins located in the cyto -plasm: keratin, type II cytoskeletal 8 (CK 8); keratin, type I cytoskeletal 18(CK 18); 60kDa heat shock protein (HSP 60); actin, cytoplasmic 2 (γ -actin); 14- 3- 3 protein beta/alpha (14- 3- 3 β /α ); and 14- 3- 3 protein epsilon ( 14- 3- 3 ε). All six proteins were overexpressed in PTC compared with normal tissues (P<0. 001 ). Meanwhile, CK 8, CK 18, HSP60, and γ -actin were overexpressed in PTC compared with bor -derline lesions ( P<0. 01). Except for CK 8, the five other proteins were overexpressed in borderline lesions compared with normal tis-sues (P<0. 001 ). Conclusion: Proteomic analysis is useful in searching for new biomarkers of PTC and thyroid borderline lesion. The ex -pression patterns of these differentially expressed proteins can be further validated using immunohistochemistry. The newly identified protein biomarkers can positively contribute to early PTC diagnosis.