It is well established that intestinal microbiota play an important role in the pathogenesis of inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease. Various methods of altering the composition of intestinal microbiota have been examined. Recent evidence suggests that the administration of select prebiotics, probiotics and synbiotics may improve the clinical outcome of patients with IBD. In addition, IBD patients are well known to carry a higher risk of developing colorectal cancer due to chronic inflammation. Therefore, probiotics and/or prebiotics may be appropriate treatments for prophylactic use due to their physiologic characteristics and lack of obvious toxicity. This review summarizes the current experimental and clinical knowledge about the role of intestinal microbiota in IBD, the prevention of carcinogenesis related to IBD, and its importance as a target for new forms of neutraceutical therapy.