In vivo magnetic resonance microscopy (MRM) of the small animal lung has become a valuable research tool, especially for preclinical studies. MRM offers a noninvasive and nondestructive tool for imaging small animals longitudinally and at high spatial resolution. We summarize some of the technical and biologic problems and solutions associated with imaging the small animal lung and describe several important pulmonary disease applications. A major advantage of MR is direct imaging of the gas spaces of the lung using breathable gases such as helium and xenon. When polarized, these gases become rich MR signal sources. In animals breathing hyperpolarized helium, the dynamics of gas distribution can be followed and airway constrictions and obstructions can be detected. Diffusion coefficients of helium can be calculated from diffusion-sensitive images, which can reveal micro-structural changes in the lungs associated with pathologies such as emphysema and fibrosis. Unlike helium, xenon in the lung is absorbed by blood and exhibits different frequencies in gas, tissue, or erythrocytes. Thus, with MR imaging, the movement of xenon gas can be tracked through pulmonary compartments to detect defects of gas transfer. MRM has become a valuable tool for studying morphologic and functional changes in small animal models of lung diseases.