We compared the frequency and extent of methylation of APC, CDKN2A, ID4, MGMT, RBP1, RUNX3, SFRP1, TIMP3, and TMEFF2 in esophageal adenocarcinoma (EAC), high grade dysplastic Barrett's from patients with adenocarcinoma (D-EAC), metaplastic Barrett's from patients without dysplasia or adenocarcinoma (BE), and histologically normal esophageal squamous epithelium. Here, RUNX3 is linked to esophageal adenocarcinoma.