Objective: To observe the apoptosis of polymorphonuclear neutrophils (PMN) in the bronchoalveolar lavage fluid (BALF) and occludin protein alteration in the alveolar epithelial cells in rats with bile duct obstruction (BDO), and analyze the relations of the two parameters with obstructive jaundice related lung injury. Methods: Seventy-two SD rats were used, 8 of them were randomly selected as normal control group, and the remaining 64 rats were equally randomized into sham group and model group. Rats in sham group underwent a sham operation and those in model group were subjected to double ligation of the common bile duct to establish a BDO model. Rats in sham group and model group were sacrificed in four batches with equal number of animals (n=8) to harvest specimens at 3, 7, 10 and 14 d after surgery, and rats in normal control group were killed to obtain specimens at random during the experimental period. The morphological analysis of the lung tissue of the rats was performed, PMN apoptosis and MMP-9 activity in the BALF, and occludin protein expression in lung tissue were determined, and the lung permeability index (LPI) was also calculated. Results: Compared with normal control group, all the parameters in sham group showed no obvious changes at each time point, and quantitative differences had no statistical significance (all P>0.05). In model group, evident lung injuries were observed, and compared with sham group, the PMN apoptosis was decreased and MMP-9 activity in the BALF was gradually increased, and the differences at each time point from 3-14 d reached statistical significance (all P<0.05); the occludin protein expression in lung tissue was decreased and LPI was gradually increased, and the differences at each time point from 7-14 d reached statistical significance (all P<0.05). Correlation analysis showed that in BDO rats, the PMN apoptotic rate was negatively correlated with MMP-9 activity (r=–0.935), the MMP-9 activity was negatively correlated with occludin protein level in lung tissue (r=–0.796), and the occludin protein level in lung tissue was negatively correlated with LPI (r=–0.800) (all P<0.05). Conclusion: In BDO rats, alveolar PMN apoptosis is decreased and MMP-9 activity is increased which may cause attenuation of occludin protein in alveolar epithelial cells, alveolar epithelial barrier damage and increased permeability. This pathological process may contribute greatly to the initiation and development of obstructive jaundice related acute lung injury.