Biomarkers are substances that can be used to indicate normal or diseased states. In clinical settings, the term biomarker generally refers to a molecular marker produced by tissues whose detection heralds a diseased state. For patients with Barrett's esophagus, there are at least three clinical settings in which the use of molecular biomarkers has been proposed including 1) stratifying the risk of neoplastic progression, 2) serving as an adjunct to aid in the diagnosis of dysplasia, and 3) predicting response to ablative therapies. Although the routine clinical use of biomarkers in any of these clinical settings is not yet recommended, it seems reasonable to assume that biomarker validation studies will be carried out in the coming years and that movement into the clinics will be inevitable. This article reviews the current progress in using biomarkers in each of the clinical settings described above with a focus on the molecular biomarkers which have advanced the farthest toward use in routine clinical practice.