Objective To search for the differences of serum proteins expression in ulcerative colitis (UC) by proteomics method and to preliminary explore the potential biological markers of ulcerative colitis. Method The serum of 30 ulcerative colitis patients and 30 healthy individuals were collected. The equal amounts of proteins in pooled serum were separated by two-dimensional gel electrophoresis (2-DE) and then compared and analyzed by image analysis software to recognize the differences of protein expression. Some spots of proteins with different expression were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS).Result There was no statistic significant in age, weight index, smoking and alcohol taking between UC group and control (P ＞ 0.05 respectively). Thirty-nine proteins with significant different expression between UC patients and healthy individuals were preliminary screened out. Nine of those spots were selected, after analyzed by MALDI-TOF-MS, it was found that the expression of haptoglobin, heat shock factor protein 2, receptor tyrosine kinase, aldehyde reductase,apolipoproteinC-Ⅲ, pericentriol material 1 increased in ulcerative colitis patients, keratinl, filamin A interacting protein 1 and tropomyosin 3 decreased. Conclusions With proteomics 2-DE and spectrometry methods, nine UC associated serum proteins were screened out and identified, which provide new molecular markers for the research of UC biological behavior.