Barrett esophagus (BE) is defined as a columnar metaplasia of the distal esophagus that develops as a result of chronic gastroesophageal reflux disease (GERD). A distinctive type of multilayered epithelium (ME) that exhibits features of both squamous and columnar epithelium has been hypothesized to represent an early, or intermediate, phase in the development of BE. The aim of this prospective study was to evaluate the prevalence and specificity of ME in mucosal biopsies of the squamocolumnar junction (SCJ) from patients who had GERD, either with or without BE. During endoscopic examination of the esophagus, 2 biopsy specimens were obtained from across the SCJ from 27 patients with BE, 12 patients who had GERD without BE, and 14 controls who had no symptoms or endoscopic or histologic signs of GERD. ME was present at the SCJ in 33%, 33%, and 0% of BE, GERD, and control patients, respectively. Compared with control subjects, the prevalence of ME was significantly higher in both GERD and BE patients (P<0.05). In GERD patients without BE, ME was always detected adjacent to areas of cardia-type mucosa composed of mucous glands. ME from GERD patients and BE patients had a similar immunophenotype, showing expression of the intestinal markers MUC2 and cdx-2 in 38% and 77% of cases, respectively. The prevalence of expression of these markers in ME was significantly different from nongoblet epithelium in control patients. Our results provide further evidence that ME may represent an early, transitional form of columnar metaplasia, and that ME may be used as a histologic marker of reflux disease in mucosal biopsies from the gastroesophageal junction region.