OBJECTIVE In this study, gastric mucosal changes and the other clinical results of patients with choledochoduodenostomy (CDD) and T-tube drainage (TTD) were compared in a follow up period of at least 5 years. METHODS The previous files of these patients were evaluated, physical examination and abdominal ultrasonography (US) and gastroscopic examination were made. Esophagus, stomach and the first two parts of the duodenum and size of the anastomosis in patients with choledochoduodenostomy were examined during gastroscopy. Two biopsies from antrum and corpus of the stomach were taken and sections stained with Hematoxylin and eosin for histopathological examination under light microscope. RESULTS In total 45 patients, 21 of them with TTD and 24 of them with CDD, were accepted for the study. No difference was present between the mean age, female/male ratio, and interval between the operation date and endoscopic control of both groups (p > 0.05). Common bile duct was evidently wide in the CDD group at the first operation (p < 0.05). In the late postoperative clinical classification of the patients, moderate group was predominant, while incidence of alkaline reflux gastritis was obviously high in the CDD group (p < 0.05). No other difference in the results was present between the two groups (p > 0.05). CONCLUSIONS According to our study long-term results of T-tube drainage is superior over choledo-choduodenostomy.