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Confocal endomicroscopy can be used to image intestinal mucosa. Epithelial gaps resulting from shedding of epithelial cells have been reported in patients. We hypothesize that the rate of epithelial cell shedding increases in patients with Crohn's disease, leading to more epithelial gaps and barrier dysfunction. In this study, we used probe-based confocal laser endomicroscopy to quantify epithelial cells and gaps in patients with Crohn's disease compared with controls. We also determined the density of epithelial gaps in a mouse model of inflammatory bowel disease—interleukin-10-deficient (IL-10−/−) mice, versus the background strain using rigid probe confocal endomicroscopy.Probe-based confocal laser endomicroscopy of the terminal ileum of both patients with Crohn's disease and controls was performed by a single endoscopist during colonoscopy. In mice, sections of the small intestine were imaged using a rigid confocal probe. Gap density was defined as the number of epithelial gaps per 1000 cells counted.In this study, we examined 6 controls (2 male and 4 female; median age 59 y) and 8 patients with Crohn's disease (5 male and 3 female; median age 42 y). The mean gap densities (±standard error) observed for the 2 groups were 17.7±5.6 and 117±33 gaps per 1000 cells, respectively (P<0.01). For control and IL-10−/− mice, the gap densities were 10.5±2.2 and 17.8±1.4 gaps per 1000 cells, respectively (P<0.01).The epithelial gap density was significantly higher in patients with Crohn's disease than controls. Gap density was also elevated in the mouse model of inflammatory bowel disease.