Colorectal cancer is a significant cause of morbidity and mortality in industrialized societies and the second most frequent cause of cancer death in the United States. Surrogate endpoint biomarkers are gaining wide acceptance in early diagnosis and short-term cancer chemoprevention trials in place of cancer endpoints. Molecular genetic biomarkers can be useful tools in identifying subjects at risk of developing cancer and screening for early cancers amenable to complete cure. They may be useful both in predicting and assessing response to a given therapy and in determining prognosis after an initial diagnosis has been made. Ideally, biomarkers should fulfill some, if not all, of the following criteria: variability of expression between phases of carcinogenesis, association with cancer risk, ability to undergo modification in response to a chemopreventive agent, and finally, permit ease of measurement. In consideration of colorectal cancer chemoprevention, several genetic biomarkers seem to meet many of these criteria, as they do exhibit distinct variability of expression at different phases of carcinogenesis, are often strongly associated with increased cancer risk (especially the hereditary/familial syndromes), are generally able to be measured relatively easily through peripheral blood sampling (germline mutations) or by colonic mucosal sampling by endoscopic techniques (somatic mutations). In some cases, genetic biomarkers have also been demonstrated to undergo modification in response to a chemopreventive agent. With further understanding of the genetic and molecular changes involved in sporadic and familial colorectal carcinogenesis, genetic biomarkers appear to hold great potential for the identification of subjects at high risk of developing colorectal cancer, as well as the development of novel chemopreventive approaches and form a promising area for further research.