The objective of the study was to evaluate the effects of ketamine on intestinal microcirculation in pentobarbital-anaesthetized rats during experimental endotoxaemia. A prospective, randomized, controlled study was carried out using 32 male Lewis rats. The animals were divided into four groups ( n = 8 each). All animals were initially anaesthetized with 60 mg/kg pentobarbital (i.p.). Group 1 served as a control (18.5 mg/kg/h pentobarbital i.v.). Groups 2 and 4 received an endotoxin intravenous infusion of 15 mg/kg lipopolysaccharide (LPS) from Escherichia coli. Groups 3 and 4 also received 10 mg/kg/h ketamine (i.v.). After 2 h of observation, the animals were examined for intestinal functional capillary density (FCD) and leukocyte adherence to the venular endothelium by means of intravital fluorescence microscopy (IVM). Subsequent to this examination, blood samples were collected to determine release of the cytokines tumour necrosis factor (TNF)- α, interleukin (IL)-1 β, IL-6 and IL-10. Endotoxaemia tended to decrease intestinal FCD (mucosa: −10.1%, muscularis longitudinalis: −2%, muscularis circularis: −9.8%) and significantly increase leukocyte adherence within submucosal venules (collecting venules: +133%, postcapillary venules: +207%; P<0.05). TNF- α, IL-1 β, IL-6 and IL-10 levels were significantly elevated following endotoxin challenge. The addition of ketamine to pentobarbital anaesthesia did not significantly affect FCD, leukocyte behaviour or cytokine levels. In conclusion, intravenous pentobarbital anaesthesia with the additional administration of ketamine did not cause alterations within the microcirculation or changes in cytokine release during endotoxaemia. In rats, the combination of pentobarbital and ketamine is suitable for use during the study of intestinal microcirculation in experimental endotoxaemia.