OBJECTIVE In order to understand the mechanisms of tumor development and identify potential new biomarkers of human papillary thyroid carcinoma (PTC), the different proteins expression were investigated and analyzed between PTC and normal thyroid tissue. METHODS By using immobilized pH gradient (IPG)-based two-dimensional gel electrophoresis (2-DE), the total proteins were separated and 2-DE maps were established for PTC and normal thyroid tissue, respectively. The differential protein spots were analyzed with Image Master 2D Elite5.0 software, then the peptide mass fingerprinting of different expressed proteins were identified by MALDI-TOF-MS/MS. Also, the functions of the differential expressed proteins were identified through Swiss-port database searching. RESULTS The 2-DE maps of PTC and normal thyroid tissue was established. Sixty differential protein spots were found by image software and seventeen proteins were identified with MALDI-TOF-MS. The biological information of these proteins was identified through Swiss-port database. In comparison with normal thyroid tissue, a total of eleven proteins were up-regulated such as Cyclin-D2, Manganese SOD and Galectin-3; while six proteins were down-regulated including Peroxiredoxin-2, Hsp70 and Hsp27. Among those up-regulated proteins, some of them were related to cell cycle control, cellular metabolism and invasion and metastasis of the tumor. CONCLUSIONS Group of differential expressed proteins between PTC and normal thyroid tissue was identified. These proteins may participate in the tumorigenesis and development of PTC through contributing to cell cycle, invasion, metastasis and cellular metabolism.