To determine whether the presence of Matrix metalloproteinases (MMPs) is associated with acute lung injury following cardiopulmonary bypass (CPB), we evaluated the activity and gene expression of matrix metalloproteinases-9 (MMP-9) and tissue inhibitor of metalloproteinase-1 (TIMP-1) of lungs using rat model of CPB. Adult male Sprague-Dawley rats were randomly divided into three groups: Group I (underwent cannulation + heparinization only); group II (underwent 60 min of normothermic CPB); and group III (underwent 60 min of normothermic of CPB, which rats received doxycycline treat by filling stomach 1 week ahead of CPB). Lung injury was evaluated histologically. The enzyme activity of MMP-9 and TIMP-1 in the bronchoalveolar lavage fluid was detected by western-blot analysis. The expression of MMP-9 and TIMP-1 in lung tissue was assessed using reverse transcriptase-polymerase chain reaction method. We found there was significantly pulmonary edema and lung injury in groups II and III compared with group I, and the histological markers of pulmonary edema in the Group III were less pronounced in comparison with Group II. The MMP-9 activity and gene expression were increased significantly, but the TIMP-1 increased slowly in group II, and the ratio of MMP-9/TIMP-1 was imbalanced severely. More significantly, the MMP-9 decreased significantly and the TIMP-1 mRNA increased gradually in group III compared with group II, and the ratio of MMP-9/TIMP-1 was improved significantly. We concluded MMP-9 might have an important role in acute lung injury following CPB. TIMP-1 increased in the rats treated with doxycycline ahead and might compensate for the activity of MMP-9. The doxycycline might have the protective effect against acute lung injury following CPB.