OBJECTIVE To elucidate the effect of a proton pump inhibitor (PPI, rabeparazole) on oesophageal bile reflux in oesophagitis after total gastrectomy. METHODS Twenty-one 8-week-old male Wistar rats were studied. They were performed oesophagoduodenostomy of total gastrectomy to induce oesophageal reflux of biliary and pancreatic juice. Five rats were performed the sham operation (Sham). On post-operative day 7, they were treated with saline (Control) (n = 8) or PPI (rabeprazole, 30 mg/kg per day, ip ) (n = 8) for 2 wk. On post-operative 21, all rats were sacrificed and each oesophagus was evaluated histologically. Oesophageal injury was evaluated by macroscopic and microscopic findings as well as the expression of cyclooxygenase-2 (COX2). We measured bile acid in the oesophageal lumen and the common bile duct. RESULTS At 3 wk after surgery, a histological study analysis revealed an increase in the thickness of the epithelium, elongation of the lamina propria and basal cell hyperplasia in the oesophageal mucosa. The macroscopic ulcer score and microscopic ulcer length of the control group were significantly higher compared to those of the rabeprazole- treated group. The expression of COX2 was significantly increased according to the immunostaining in the control group compared to rabeprazole- treated group. Although there was no difference between the control and PPI groups in the total bile acid in the common bile duct, the bile acid activity in the oesophageal lumen was significantly decreased in the rabeprazole- treated group due to augmentation of the duodenal motor complex. CONCLUSIONS With this model, rabeprazole is good effect for reflux esophagitis after total gastrectomy from bile reflux. Bile acid is an important factor in the mucosal lesion induced by duodenal reflux.