Background Intestinal ischaemia-reperfusion, a frequent occurrence during cardiac surgery with cardiopulmonary bypass (CPB) induces a systemic inflammatory reaction. We hypothesised that ischaemia-reperfusion following prolonged CPB could increase intestinal permeability and thus, lead to endotoxin translocation from the intestine to the bloodstream. Material and Methods Patients subjected to coronary artery bypass grafting with CPB were included: Group 1 (CPB >= 90 minutes) or Group 2 (CPB <90 minutes). Intestinal Fatty Acid Binding Protein (I-FABP), TNF alpha, IL6, IL8, and endotoxin levels were measured before the induction of general anaesthesia (T1), at 6 (T2), and 24 hours (T3) after surgery. Results The low level of I-FABP at T1 increased for every patient in Group 1 at T2 (from 1015.5 pg/mL to 2608.5 pg/mL, p=0.02) and in Group 2 (from 1123.5 pg/ml to 2284.0 pg/ml, p<0.001). Furthermore, at T3, the I-FABP level was over three times higher in Group 1 than in Group 2 (2178 pg/mL vs 615 pg/mL; p<0.001). I-FABP correlated with CPB time (R=0.6, p<0.001) at T3. After surgery, endotoxins were elevated in 73% of patients in Group 1 and in 32% in Group 2 and correlated with CPB time (at T2, R=0.5, p=0.002; at T3, R=0.4, p=0.016). Conclusions The duration of CPB is linked to the release of biomarkers that indicate ischaemic-reperfusion damage to the gastrointestinal mucosa and endotoxaemia. I-FABP assay may help to identify patients presenting with intestinal damage, who are at risk of bacterial translocation.