Barrett's esophagus is a metaplastic condition that occurs in patients with gastroesophageal reflux disease (GERD) and its importance lies in its potential to develop adenocarcinoma of the esophagus. The diagnosis of Barrett's esophagus is based on finding of intestinal metaplasia of at least 3 cm of the distal esophagus. The diagnosis of intestinal metaplasia of less than 3 cm of the distal esophagus is controversial, regarding implications with GERD, adenocarcinoma, and Helicobacter pylori. The aims of the study were to determine the prevalence of intestinal metaplasia in the distal esophagus in patients with short segments of esophageal columnar-appearing mucosa (less than 3 cm), diagnosed endoscopically, in two groups of patients, with and without symptoms of GERD. In total, 97 patients were examined, with endoscopic finding of esophageal columnar-appearing mucosa less than 3 cm. From the total, 52 patients had symptoms of GERD and 45 patients were without these symptoms. These patients were subjected to distal esophageal biopsies obtained immediately below the epithelial transition. The biopsies were stained with hematoxylin-eosin and alcian blue at pH 2.5. Urease test for H. pylori detection in two fragments of gastric antrum was carried out. The presence of intestinal metaplasia in the distal esophagus was diagnosed in 16 (30.8%) patients in the GERD group and 12 (26.7%) patients without GERD symptoms. No statistical differences were observed (P = 0.82; 95% CI: 0.61-2.17). The variables sex, mean age and positivity for H. pylori did not show statistical differences. This study diagnosed high prevalence of intestinal metaplasia in the distal esophagus with columnar-appearing mucosa, less than 3 cm, with no statistical differences in the two groups studied with and without GERD symptoms.