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Objective: To comparatively study the different effects of open heart surgery on brain tissues of patients with congenital and rheumatic heart disease. Methods: Forty patients with congenital heart disease (CHD, CHD group, n=20) or rheumatic heart disease (RHD, RHD group, n=20) underwent on-pump (cardiopulmonary bypass, CPB) heart-beating open heart surgery. Blood samples before CPB, and 20 minutes, 1 hour, 24 hours and 7 days after CPB were collected, and the levels of neuron-specific enolase (NSE) and protein S-100b in the plasma were determined with enzyme-linked immunoadsorbent assay (ELISA), respectively. All the patients were examined with electroencephalogram (EEG) before and 1 week after operation. The changes of NSE, S-100b and EEG compared to verify the difference of postoperative cerebral injury between CHD cases and RHD cases. Results: The plasma level of S-100b increased significantly 20 minutes after CPB and was still higher than the preoperative level at 24 hours after operation in both groups (P