Gene chip methods are applied to the study of gene expression. The differentially expressed genes in different specimens may be detected with parallel analysis by gene chip, which has greatly improved the traditional experiments in that only a single or several gene expressions need to be observed for each test, thereby speeding up the identification of differentially expressed genes and the construction of differential expression profiles. Many studies have applied this technology for Barrett's metaplasia and adenocarcinoma, and identified a number of candidate genes useful as biomarkers in cancer staging, prediction of recurrence, prognosis and treatment selection. This review described the gene expression profile and molecular changes related to Barrett's metaplasia and adenocarcinoma of the esophagus, with emphasis on its prognostic value and possibilities for targeted therapy in a clinical setting.