Objective: Barrett's esophagus (BE) is the major risk factor for esophageal adenocarcinoma (EA). BE has a low risk of progression to EA, being imperative to identify markers to stratify the risk. Our aim was to look for potential early biomarkers of BE malignant progression. Method: Three available microarray datasets were analyzed with R Statistical Computing software complemented with Bioconductor. Biomarker prioritization included: 1) Expression Barcode 2.0; 2) filtering using differential expression analysis. Candidate genes were validated by qRT-PCR on RNA from paraffin embedded samples (RNA-PES) of BE patients with high-grade dysplasia/ADC diagnosed during surveillance and of their index endoscopy dysplasia-free samples. As controls, we used samples from BE patients who have not progressed. Results: Under conservative criteria, we identified 19 upregulated genes that distinguish EA-progressed from nonprogressed BE samples. A second filter, followed by qRT-PCR validation, trimmed the candidates to 2 markers (WWTR1 and CYR61). qRT-PCR on time-series RNA-PES of EA-progressed and EA-free BE samples showed these genes are up-regulated years before the development of EA as compared to patients who did not developed EA. Conclusion: WWTR1 and CYR61 were identified as early risk markers for BE neoplastic progression and may have a potential role in BE risk stratification.