Objective To identify synovium-associated proteins of by analyzing proteome of FLS between RA patients and traumatic arthritis. Methods The total protein of FLS from 3 patients of RA and 6 normal controls were separated by 2-DE. The differentially expressed proteins were identified by MALDI-TOF-MS. Results The 2-DE image results showed that there were many proteins differentially expressed in FLS from RA and control. A total of 33 differential proteins that were up-regulated in RA as compared with controls were selected and 30 proteins including pyruvate kinase isozymes M1/M2, α-enolase, protein disulfide-isomerase A3 precursor, glutathione transferase, peroxiredoxin 1, ubiquitin-conjugating enzyme E2K, platelet-activating factor acetylhydrolase IB, dihydropyrimidinase-related protein 2, adenosine kinase, transaldolase, δ-δ-dienoyl-CoAisomerase, 26S protease regulatory subunit 6A, annexin All, tryptophanyl-tRNA synthetase isoform b, lamin-A/C, myomesin-1 isoform b, ruvB-like 1, actin-cytoplasmic 1, T-complex protein 1, stress-70 protein, mitochondrial precursor, α-crystallin B chain, 78 000 glucose-regulated protein, PSME4, SELENBP1 and so on. Conclusion The differentially expressed proteins are present in FLS from RA and control, which may be the synovium biomakers and involved in pathogenesis of RA.