OBJECTIVE To evaluate the influence of preoperatively selected gut decontamination (SGD) on intestinally derived endotoxemia(ETM) in patients with rheumatic heart disease undergoing valve replacement operation with cardiopulmonary bypass(CPB). METHODS Thirty patients were randomly divided into control group and SGD group. The patients in control group underwent preoperative bowel preparation, i.e, diet preparation and enema. The patients in SGD group were administrated 100 mg Tobramycin, 40 mg garlicin and 20% Lactulose for 10 ml three times per day for 3 days besides routinely preoperative bowel preparation. Bacteria cultivation and identification and Gram staining of feces in both groups were used to evaluate species of intestinal flora and their ratios. The levels of endotoxin, D-lactate, TNF-alpha and complement 3 were determined at four time points of anesthetic induction, CPB end, 2 h after CPB, 24 h after CPB. And the related clinical biochemical and clinical markers were recorded. RESULTS Aerobic gram-negative bacilli (AGNB) ratio in post-SGD group decreased significantly as compared with that in control group and pre-SGD group (P less than 0.05). The level of D-lactate reduced significantly at time points of anesthetic induction and 2 h after CPB (P less than 0.05). Endotoxin levels of patients in both groups elevated significantly after CPB (P less than 0.05), and endotoxin levels of the patients in SGD group decreased significantly at points of CPB end (P less than 0.01) and 24 h after CPB (P less than 0.05) compared with those in control group. The levels of TNF-alpha and complement 3 were similar in both groups as well as clinical and biochemical markers. CONCLUSIONS CPB induces endotoxemia, while the regime of SGD is an effective way to prevent endotoxemia but may not affect activation of inflammatory media and clinical outcomes.