Gastrointestinal complications following cardiopulmonary bypass (CPB) are relatively uncommon, but are associated with a high mortality rate. Impairment of bowel perfusion during and following CPB may serve as a trigger for the development of multiorgan failure. The aim of our study was the development of a new animal model allowing quantitative analysis of small bowel microcirculation during and after CPB. Twelve Landrace pigs served as laboratory animals. A 15-cm loop of the terminal ileum was exteriorized for microscopic observation. In 6 animals, a normothermic, partial left heart bypass (pLHB) was established for 2 h with a flow rate of 2,000 ml/min. Arterioles, collecting venules and the capillaries of the small bowel were recorded for the analysis of the microcirculation. All parameters were recorded prior to, during pLHB and up to 2 h after weaning off the bypass. Six sham operated animals served as controls. Despite unchanged hemodynamics, pLHB leads to microvascular perfusion disturbances of the small bowel. In pLHB animals, blood cell velocity in postcapillary venules (30–70 µm) was significantly decreased during and following bypass. Capillary density was also reduced during bypass and decreased even further after pLHB to only 30% of the control values. With this new large animal model for quantitative assessment of microvascular perfusion of the small bowel during CPB, it could be clearly demonstrated that partial normothermic left heart bypass leads to a significant disturbance of the small bowel microcirculation even under stable hemodynamic conditions.