It is well understood that intestinal microbiota play an important role in the pathogenesis of inflammatory bowel disease (IBD). In addition, IBD patients are well known to have a higher risk of developing colon cancer due to chronic inflammation. Recent evidence suggests that manipulation of microbiota improves the clinical outcome of patients with IBD and may reduce onset of colon cancer without obvious toxicity. This review summarizes the current experimental and clinical knowledge about the role of intestinal microbiota in IBD and colon cancer, and the nutraceutical therapy for colon cancer.