Claudins are transmembrane proteins constituting one of three tight junction protein families. There are 24 members of the claudin family identified, differently expressed in various cells/tissues and among species. In patients with inflammatory bowel disease (IBD), site and disease activity dependant changes in expression of certain claudins has been noted. The aim of the study was to explore expression of claudins in the mouse models of IBD and to compare it to claudin expression in human disease. The expression of several sealing claudins that are present in colon of humans and rodents has been evaluated by immunohistochemistry. A decrease in claudin 1 expression was observed in a chronic mouse DSS model and adoptive transfer model of colitis, as it has been reported in human disease. Claudin 3 expression was not altered in the non-inflamed mucosa. Nevertheless, a subset of claudin 3 was internalized into cytoplasm of absorptive cells in inflamed mucosa in a chronic DSS model. In an adoptive transfer model of IBD, 8 weeks post-transfer, a reduction in claudin 3 expression was noted in surface colon epithelium as noticed in patients with Crohn's disease and ulcerative colitis. Claudin 8 expression decreased in the upper part of crypts, as is reported in patients with Crohn’s disease. A subset of crypt base cells became strongly positive. Finally, a decrease in claudin expression in inflamed mucosa of human biopsies from patients with ulcerative colitis (UC) was observed. In conclusion, it was shown that claudin 1, 3 and 8 expression pattern/ intensity is altered in the mouse models of IBD in a same manner as observed in human biopsies from UC patients and described in patients with Crohn's disease.