Background/aims: Gastroesophageal reflux disease is seen frequently in patients with progressive systemic sclerosis. The aim of the present study was to determine the prevalence of intestinal metaplasia-squamocolumnar junction in patients with progressive systemic sclerosis and to investigate the association with gastroesophageal reflux disease. Methods: Thirty-one patients with progressive systemic sclerosis (Group A), 58 patients with gastroesophageal reflux disease -without progressive systemic sclerosis (Group B) and 36 patients without progressive systemic sclerosis or gastroesophageal reflux disease (Group C) were prospectively enrolled into this study. Biopsies were taken from the antrum, body, squamocolumnar junction (Z-line), and from the esophagus (3 cm above the Z-line). All biopsies were independently evaluated by two pathologists who were unaware of the diagnosis. Results: We found that grade C-D esophagitis, esophageal stricture and Barrett's esophagus were statistically significantly higher in Group A (p<0.05). Intestinal metaplasia at squamocolumnar junction was detected in 31% of Group A, in 32% of Group B and in 29% of Group C patients (p>0.05), and prevalence of Helicobacter pylori was 61%, 67% and 38% in Groups A, B and C, respectively. Prevalence of Helicobacter pylori was similar in Group B and Group A, and significantly higher in Group B than Group C. Within each group, no significant relationship was detected between intestinal metaplasia at squamocolumnar junction and gender, age, smoking, alcohol consumption, body mass index, gastric atrophy, and prevalence of Helicobacter pylori. Conclusions: Patients with progressive systemic sclerosis have a higher tendency to the more severe forms and complications of gastroesophageal reflux disease including Barrett's esophagus than in those without progressive systemic sclerosis. However, there was no difference in the prevalence of intestinal metaplasia at squamocolumnar junction between groups, and it can he pointed out that intestinal metaplasia at squamocolumnar junction might not be related with gastroesophageal reflux disease.