In vivo lung‐targeted VEGF gene inactivation results in pulmonary cell apoptosis, airspace enlargement, and increased lung compliance consistent with an emphysema‐like phenotype. The predominant hypothesis for the cause of lung destruction in emphysema is an imbalance between active lung protease and anti‐protease molecules. Therefore, we investigated the role of protease (e.g., matrix metalloproteinases—MMPs) and anti‐protease (e.g., tissue inhibitors of metalloproteinases—TIMPs) expression in contributing to the lung structural remodeling observed in pulmonary‐VEGF‐deficient mice. VEGFLoxP mice instilled through the trachea with an adeno‐associated virus expressing Cre recombinase (AAV/Cre) manifest airspace enlargement and a greater (P < 0.05) mean linear intercept (MLI: 44.2 ± 4.2 µm) compared to mice instilled with a control virus expressing LacZ (31.3 ± 2.5 µm). Airspace enlargement was prevented by the continuous administration of the general MMP inhibitor, doxycycline (Dox) (Cre + Dox: 32.6 ± 2.5 µm), and MLI values were not different from either control (LacZ + Dox: 30.5 ± 1.2 µm). In situ magnetic resonance imaging of VEGF gene inactivated mouse lungs revealed uneven inflation, residual trapped gas volumes upon oxygen absorption deflation/re‐inflation, and loss of parenchymal structure; effects that were largely prevented by Dox. Five weeks after AAV/Cre infection Western blot revealed a 9.9‐fold increase in pulmonary MMP‐3, and 2‐fold increases in MMP‐9 and TIMP‐2. However, the increase in MMP‐3 was prevented by Dox administration and was associated with a 2‐fold increase in serpin b5 (Maspin) expression. These results suggest that doxycycline treatment largely prevents the aberrant lung remodeling response observed in VEGF‐deficient mouse lungs and is associated with changes in protease and anti‐protease expression. J. Cell. Biochem. 104: 525–535, 2008. © 2008 Wiley‐Liss, Inc.