Background: Although some reports suggest that bronchoscopy induces bacterial translocation (BT), the mechanisms of BT remain unclear. Objective: We aimed to assess whether bronchoscopy or hypoxemia during bronchoscopy is responsible for BT. Methods: We evaluated 24 rats divided into three subgroups: the control group (group 1, n = 8); the rigid bronchoscopy group (group 2, n = 8), and the group receiving bronchoscopy + mechanical ventilation (group 3, n = 8). Oxygen saturation (SaO2) was measured during the bronchoscopic procedure. Blood and tissue cultures from mesenteric lymph nodes (MLNs), liver, spleen and cecal contents were obtained 24 h following bronchoscopy. Results: In group 2, SaO2 was significantly lower than in groups 1 and 3 (p < 0.01). In group 2, BT significantly increased (6/8, 75%; p < 0.01 vs. group 1, and p < 0.05 vs. group 3). The main site of translocation was MLNs (6/8, 75%) in group 2, while BT was detected in only 1 rat in group 3 (1/8, 12.5%). Conclusion: Hypoxemia during rigid bronchoscopy resulted in intestinal mucosal damage in a rat model. Hypoxemia may have been the trigger for BT from the intestine following bronchoscopy.