Colorectal cancer is a significant clinical problem for patients with long-standing ulcerative colitis and Crohn's disease. Traditional risk factors include long disease duration and greater extent of colonic disease, but newer factors such as associated primary sclerosing cholangitis, folate deficiency, and family history of colon cancer may help to refine risk stratification. Molecular pathogenesis of colitis-associated colon cancer shares some of the same genetic abnormalities as sporadic colon cancer, but the timing of certain alterations suggests different carcinogenic pathways. Some molecular alterations show promise as complementary markers to dysplasia. Clinical studies of colonoscopic surveillance indicate that colon cancers can be detected early and that mortality may therefore be improved. A suggested surveillance strategy is proposed.