To discuss the differences in protein expression among tuberculosis pleural effusion (TBPE), malignant pleural effusion (MPE) and transudative pleural effusion (TSPE). We recruited 50 patients with pleural effusion, including 20 TBPEs, 17 MPEs and 13 TSPEs. Using the two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS), we acquired the peptide mass finger printings (PMFs) of featured proteins. Then, we identified characteristic proteins by searching in the protein databank of the National Center of Biotechnology Information (NCBI) and assessed their diagnostic significance. We found five characteristic proteins: C1-inhibitor (C1-INH), transthyretin (TTR), human complement fragment 3b (C3b), human ceruloplasmin (CP), and Z34c protein fragment Fc (Z34c-Fc). C1-INH shows a high expression in TBPE and a low expression in MPE while TTR and C3 show low expression in TBPE and high expressions in MPE. Z34c-Fc and CP have a higher expression in TBPE than in TSPE. No common characteristic protein was found between MPE and TSPE. Statistic analysis consisted of paired t-tests and the difference between them is significance (P<0.05). C1-inhibitor (C1-INH), transthyretin (TTR), human Complement fragment 3b (C3b), human Ceruloplasmin (CP) and Z34c protein fragment Fc (Z34c-Fc) may provide an additional perspective in the differential diagnosis of PE.