For patients found to have intestinal metaplasia at the gastroesophageal junction, technical problems can make it difficult to distinguish short-segment Barrett's esophagus from intestinal metaplasia of the gastric cardia. Whereas the risk of malignancy for the former condition seems to be higher than that for the latter, the distinction between these conditions can have practical clinical implications. Immunostaining for cytokeratins has been proposed as a means to distinguish intestinal metaplasia of esophageal and gastric origins. We review recent data on this issue, and conclude that immunostaining for cytokeratins has no clear advantages over other biomarkers that have been proposed for identifying Barrett's esophagus (e.g., mucin histochemistry, mAb Das-1 immunoreactivity). Presently, the importance of intestinal metaplasia at the gastroesophageal junction remains unclear, and the clinical utility of biomarkers in distinguishing short-segment Barrett's esophagus from intestinal metaplasia of the gastric cardia has not yet been established.