There are inherent problems with the endoscopic and pathologic criteria for columnar-lined esophagus (CLE). Furthermore, the clinical and biological significance of an irregular squamocolumnar junction (SCJ) is unclear. The aim of this study was to evaluate the association between histologic features in SCJ biopsies and CLE and to gain insight into the significance of an irregular SCJ. The study was a cross-sectional analysis of 2176 mucosal biopsies of the SCJ from 544 patients in a large prospective community clinic-based study of gastroesophageal reflux disease in Washington State. Biopsy samples were evaluated blindly for a wide variety of histologic features, such as the presence and type of mucosal glands, submucosal glands and ducts, goblet cells, multilayered epithelium (ME), inflammation, and buried columnar epithelium. Histologic findings were correlated with the endoscopic findings (normal Z-line, irregular Z-line, or CLE) and evaluated by logistic regression and receiver operating characteristic analysis.Five histologic features were associated with CLE: pure mucous glands, ME, presence of goblet cells, ≥50% of crypts with goblet cells, and buried columnar epithelium. Pure oxyntic glands were inversely associated with CLE. The features most strongly related to CLE included biopsies with ≥50% of crypts with goblet cells, ME, and mucosal gland type (area under the curve=0.71; 95% confidence interval=0.66-0.76). Patients with an irregular Z-line were histologically similar to those with CLE. Certain histologic features in biopsies of the SCJ are associated with the presence of CLE. Irregularity of the Z-line is probably indicative of ultrashort segment CLE, instead of being a potential variation of normal.