Objective To determine if aquaporin1 (AQP1) and aquaporin5 (AQP5) are expressed in the alveolar-capillary membrane in rats, and to investigate the changes of AQP1 and AQP5 expression in the rat with acute lung injury. Methods The distribution of AQP1 and AQP5 in alveolar capillary membrane was investigated by immunohistochemistry and immunoelectron microscopy with affinity-purified antibodies to human AQP1 and AQP5. The possibility that alveolar capillary membrane AQP1 and AQP5 undergo altered regulation was studied by a rat model established using intra-tracheal instillation of lipopolysaccharide (LPS). Results Immunolabelling showed that AQP1 was stained primarily in the microvascular endothelium of normal lungs, while AQP5 was expressed in type I pneumocytes. Immunohistochemical analysis showed a significant decrease in the expression of AQP1 and AQP5 in injured lungs at 4-48 h after LPS instillation. AQP1 protein was resumed partly at 24 h after LPS instillation and steroid administration, whereas AQP5 was unchanged. Conclusions The decreased expressions of AQP1 and AQP5 in injured lungs suggest that both of them may play a role in abnormal fluid transportation.