Aim There are common findings between Behcet's disease (BD) and celiac disease (CD) based on similar immunological pathogenesis and there is only limited data available investigating the link between these two diseases. Furthermore, documented gastrointestinal (GI) involvement with marked upper GI symptoms in BD has been rarely reported. The aim of this study was to assess the prevalence of CD and to evaluate endoscopic findings in Turkish BD patients. Methods A total of 210 BD patients were included in the study. All patients underwent serological testing for anti-gliadin and tissue transglutaminase antibodies. Endoscopic examinations were performed in 190 patients who accepted upper GI system endoscopy. Multiple biopsies were taken from the second portion of the duodenum in patients with positive serological assessment for CD. Results A total of 4.2% of patients with BD had positive anti-gliadin and tissue transglutaminase antibody immunoglobulin A (IgA) and IgG antibodies. The prevalence of biopsy-confirmed CD was 1.05% in Turkish BD patients. The most common endoscopic findings of patients with BD were found to be antral gastritis, duodenitis and esophagitis. Conclusion Although BD and CD share many similar clinical manifestations, our results did not support a possible association between these two diseases.