Abstract： Objective To study the molecular mechanism of pathologic states related to cardiopulmonary bypass (CPB) and screen the differential proteins from the serum before and after CPB in the open heart surgery patients. Methods By the twodimensional gel electrophoresis (2DE), we took the blood samples from each of the sixteen open heart surgery patients 30 minutes before CPB, 1 hour after CPB, and 24 hours after CPB. The protein spots were analyzed by the PDQuest image analysis software and the differential protein spots were identified by matrixassisted laser desorption/ionizationtime of flightmass spectrometry (MALDITOF-MS). Then, enzymelinked immunosorbent assay (ELISA) was used to determine the expression level of serum amyloid A protein (SAA) in the serum of healthy people and the enrolled patients before and after CPB. Results Through 2DE in combination with massspectrometry, 7 proteins altered in expression were identified, including SAA, haptoglobin (HPT), leucinerich alpha2-glycoprotein (A2GL), hemoglobin subunit beta (HBB), serine/threonineprotein phosphatase 2A -regulatory subunit B″ subunit gamma (P2R3C), transthyretin (TTHY), and T-complex protein 11-like protein2 (T11L2). ELISA analysis showed that SAA levels in healthy people and the open heart surgery patients 30 minutes before CPB were not statistically different (t=-1.955, P=0.056), while the SAA level rose from 54.47±48.32 μg/ml 30 min before CPB to 1 017.78±189.92 μg/ml 24 hours after CPB in the serum of open heart surgery patients． Conclusion The results of this pilot study illustrate that SAA, HPT, A2GL, HBB, P2R3C, TTHY and T11L2 may be the molecule markers of pathologic state related to CPB. Acute phase reaction happens intensively after CPB in human body.