OBJECTIVE The purpose of this study was to identity protein expression patterns of fibroblast-like synoviocytes (FLSs) derived from the synovial tissue of patients with rheumatoid arthritis (RA) and osteoarthritis. METHODS Two-dimensional gel electrophoresis (2-DE) in combination with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) was used to visualise and identify differential cellular protein expression profiles in FLSs between RA and control groups. Western-blot analysis was performed to further verify selected differentially-expressed proteins. RESULTS A total of 1633 and 1603 protein spots were examined in synovial FLSs of RA patients and controls, respectively. Ninety-two spots in the RA group were statistically over- or under-expressed compared with controls. Among them, 33 proteins over-expressed by more than 3-fold were then identified by MALDI-TOF-MS analysis. These proteins included enzymatic and structural proteins (e.g. PKM1/M2, α-enolase, ERp60, lamin-A/C), signal transduction proteins (e.g. annexin 11, peroxiredoxin 1, TrpRS), heat-shock/chaperone proteins (e.g. TCP-1, GRP75, HspB5, Bip) and some unknown protein species. Three proteins, namely α-enolase, GRP75 and PKM2, were verified by Western blot and the results were found to be consistent with proteomic analysis. CONCLUSIONS The differentially expressed proteins identified in RA synovial FLSs might be candidate RA-associated proteins and may prove to be promising diagnostic indicators or new therapeutic targets for RA.