Barrett's esophagus develops when refluxed gastric juice injures the esophageal squamous lining and the injury heals through a metaplastic process in which intestinal-type columnar cells replace squamous ones. The progenitor cell that gives rise to Barrett's metaplasia is not known, nor is it known why the condition is predisposed to malignancy. We studied the contribution of bone marrow stem cells to the development of Barrett's esophagus in an animal model. Twenty female rats were given a lethal dose of irradiation followed by tail vein injection of bone marrow cells from male rats. Ten days later, the female rats were randomly assigned to undergo either esophagojejunostomy, a procedure that causes reflux esophagitis with intestinal metaplasia, or a sham operation. The rats were killed at 8 weeks and serial sections of the snap-frozen esophagi were cut and mounted on slides. The first and last sections were used for histological evaluation and the intervening sections were immunostained for cytokeratin to identify epithelial cells and analyzed for Y chromosome by fluorescence in situ hybridization (FISH). Histological evaluation of the esophagi from rats that had esophagojejunostomy revealed ulcerative esophagitis and multiple areas of intestinal metaplasia. FISH analyses showed that some of the squamous epithelial cells and some of the columnar epithelial cells lining the glands of the intestinal metaplasia were positive for Y chromosome. These observations suggest that multi-potential progenitor cells of bone marrow origin contribute to esophageal regeneration and metaplasia in this rat model of Barrett's esophagus.