Background One-anastomosis gastric bypass/mini-gastric bypass (OAGB/MGB) remains controversial because it may cause chronic biliary reflux (BR). The risk of developing esogastric cancer due to BR after OAGB/MGB is based on the results of experimental rat studies using esojejunostomy (EJ). The aim of this study was to analyze the potential long-term consequences of BR on the esogastric mucosae in OAGB/MGB-operated rats and to compare these results to those from the use of EJ. Methods Wistar rats received OAGB/MGB ( n  = 16), EJ ( n  = 16), and sham ( n  = 8) operations. Mortality and weight changes were evaluated throughout the experiment. BR was measured using magnetic resonance imaging (MRI). Rats received follow-ups for 30 weeks. A double-blinded histological analysis was performed in the esogastric segments. Results BR was diagnosed in OAGB/MGB and EJ rats using the MRI technique; no BR occurred in the sham group. After a 30-week follow-up, no incidences of dysplasia or cancer were observed in the three groups. Additionally, esophageal intestinal metaplasia and mucosal ulcerations were observed in 41.7% and 50% of EJ rats, respectively, and no incidences of these conditions were observed in OAGB/MGB and sham rats. The incidence of esophagitis was significantly higher and more severe in the EJ group compared to those in the OAGB/MGB and sham groups (EJ = 100%, OAGB/MGB = 16.7%, sham = 8.3%; p  < 0.001). Conclusions After a 30-week follow-up period, OAGB/MGB rats did not develop any precancerous or cancerous lesions when more than 40% of EJ rats had intestinal metaplasia.