The histologic diagnosis of Barrett's esophagus requires the presence of goblet cells, but this finding may not be the earliest indicator of intestinal metaplasia. We used immunohistochemistry to detect Cdx2, a transcriptional regulator important in the early differentiation and maintenance of intestinal epithelium, in 134 esophageal biopsy or resection specimens, including 62 with junctional-type epithelium (13 of which had equivocal histologic features of Barrett's epithelium), 34 with Barrett's epithelium without dysplasia, and 38 with Barrett's epithelium and dysplasia or carcinoma (13 low-grade dysplasias, 19 high-grade dysplasias, and 6 adenocarcinomas). We also performed PAS-alcian blue staining (pH 2.5) on adjacent sections. Cdx2 was observed in all cases of Barrett's epithelium. In some dysplasias (chiefly high-grade) and adenocarcinomas, there was diminution or focal loss of detectable protein. Cdx2 was detected in 20 of 62 cases (30%) of junctional-type epithelium, including 10 of 13 (77%) with equivocal histologic features of Barrett's epithelium. Acid mucin was present in goblet cells and non-goblet columnar cells in all cases of Barrett's esophagus and in non-goblet columnar cells in 48 of 62 cases (77%) with junctional-type epithelium only, including 17 of 20 (85%) that were Cdx2 positive and 31 of 42 (74%) that were Cdx2 negative. These results provide evidence that Cdx2 protein is a sensitive marker of intestinal metaplasia in the upper gastrointestinal tract and may be useful in detecting histologically equivocal cases of Barrett's esophagus. Cdx2 is present in dysplasia and adenocarcinoma, with some loss of protein primarily in high-grade dysplasia and adenocarcinoma. Acid mucin in non-goblet columnar cells is a common feature of Barrett's and junctional-type epithelium and may not always be indicative of intestinal metaplasia.