Intestinal metaplasia is a prerequisite criterion for the diagnosis of Barrett's metaplasia and the sole columnar esophageal lining associated with malignancy. It is recognized by the presence of goblet cells, but columnar non-goblet elements, producing gastric or intestinal proteins, are the prevalent cell population. The cellular heterogeneity of Barrett's metaplasia is well documented but the relationship between the distinct cell subtypes and neoplasia is unclear. Our aim was to clarify the relationship between the different metaplastic populations and malignancy in order to investigate putative markers for risk stratification of Barrett's patients. We studied 46 columnar-lined esophageal segments, 15 with associated adenocarcinoma. The presence of the gastric, MUC5AC and MUC6, and the intestinal, MUC2, proteins was evaluated in metaplastic (columnar and goblet) and neoplastic cells. In neoplasia MUC5AC and MUC6 were detected in 100% and 86.6% of the cases, respectively. In metaplasia there were no differences in MUC5AC and MUC6 immunoreactivity, between cases with and without associated neoplasia, except for goblet elements producing MUC6 that were exclusive of metaplasia adjacent to adenocarcinoma (P < 0.05). MUC2 was present in 86.6% of the neoplasia. In metaplasia it was restricted to Barrett's cases and was more frequent in areas with intestinal metaplasia. Columnar-lined esophagus without intestinal metaplasia did not express MUC2. Our study suggests a relationship between the metaplastic population with gastric phenotype and malignancy, and points to the involvement of columnar as well as goblet elements in tumorigenesis. The association between goblet cells aberrantly producing MUC6 and the presence of neoplasia suggests they may be useful for risk stratification.