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The effects of sepsis on gut mucosal blood flow have not been fully clarified. We designed an experiment to explicitly describe the effects of sepsis on gut mucosal blood flow in rats using an advanced intravital microscopy technique.This work was performed as a prospective, controlled laboratory experiment. Twenty-four hours after sham laparotomy or laparotomy and caecal ligation and perforation to create sepsis, rats were anaesthetized and their lungs mechanically ventilated (n =7 per group). Intravital videomicroscopy was performed on 6–12 villi of ileum mucosa. Video recordings were analysed off-line using computerized image analysis.Intercapillary area size (inversely related to capillary density) was increased in sepsis as compared with the control group (941 ± 92 vs. 669 ± 79 μm2, P < 0.05). In the central villus arteriole, blood flow was similar between groups (control: 3.5 ± 0.4 nL min–1; caecal ligation and perforation group: 3.6 ± 0.5 nL min–1). There were no relevant changes in arteriolar red cell velocity and diameter.In the gut mucosa of rats, sepsis resulting from caecal ligation and perforation depressed the perfused capillary density without affecting blood flow in the central villus arteriole. Mucosal hypoperfusion at the level of the capillary networks may occur in the presence of precapillary shunting in the villus microcirculation.