The aim of this prospective study was to determine the feasibility of intestinal endoluminal microdialysis as a new method for clinical monitoring of the adequacy of splanchnic perfusion in the large bowel. A microdialysis catheter for continuous lactate, glycerol, glucose and pyruvate measurements attached to a tonometric catheter was placed into the lumen of the recto-sigmoid junction prior to surgery in 13 patients undergoing elective cardiac surgery with cardiopulmonary bypass (CPB). Lactate was also measured in blood and muscle. CPB was associated with a 10-fold increase in luminal lactate from 0.16 (0.01) to 1.67 (0.38) mmol.l−1 (p < 0.001). Muscular lactate increased from baseline levels 1.20 (0.21) to 1.77 (0.36) mmol.l−1 during CPB (p = 0.01), but the muscular lactate–pyruvate ratio remained unchanged. Arterial lactate increased only slightly from 0.9 (0.05) to 1.1 (0.06) mmol.l−1 (p = 0.027) during CPB. Increased lactate concentrations in the large bowel during CPB are suggestive of local lactate production consistent with impaired oxygen delivery. Intestinal endoluminal microdialysis is a potential clinically applicable method for monitoring intestinal metabolism. Combined with tonometry, microdialysis provides the opportunity to monitor both circulation and metabolism in the rectal mucosa.