Barrett’s esophagus (BE) is a pathologically confirmed intestinal metaplasia (CM) of the distal esophagus. BE is recognized as a potential complication of gastroesophageal reflux disease (GERD) and a premalignant condition with a high risk of neoplastic progression. The aim of this study was to compare the morphology of biopsied BE segments and CM segments extending < 1 cm and > 1 cm above the gastroesophageal junction (GEJ), as well as to perform the immunohistochemical analysis of biopsies with BE and CM > 1 cm above GEJ with or without dysplasia. The study recruited 92 patients with GERD: 42 patients with BE, 24 patients with CM > 1 cm above GEJ (С0М1.5–С13M14) and 26 patients with CM < 1 cm above GEJ (С0М0.3–0.8). Comparative analysis of tissue morphology revealed an association between the reactive changes in the epithelium and the severity of esophagitis in all groups. Reactive changes were detected significantly more often in BE segments than in CM segments > 1 cm (Mann-Whitney U, p < 0.05). Eight patients with BE (19.05%) were found to have low-grade dysplasia. One patient with CM > 1 cm above GEJ (4.2%) had high-grade dysplasia with cardiac-type metaplasia and immunohistochemical features of submorphological enteralization. Immunohistochemical testing for the intestinal and gastric markers of cell differentiation revealed the signs of submorphological enteralisation in all esophageal specimens with cardiac and fundic type metaplasia and in the specimens with BE in the areas lacking goblet cells.