The etiology of chronic inflammatory bowel diseases (IBD) such as Crohn's disease and ulcerative colitis is still unknown. Recent studies including animal models of intestinal inflammation have identified interactions between the mucosal immune system, host genetic susceptibility and environmental factors, including normal intestinal microflora. Although the ideal animal model of IBD has not been found, each model can study pathogenetic factors such as acute intestinal injury and healing, acute and chronic inflammation, regulation by key cytokines, T-lymphocyte mediation, the role of luminal bacteria, immunoregulatory factors and genetic susceptibility. The relevance of these studies for the treatment of IBD is also discussed.