Label-free molecular imaging is a promising utility to study tissues in terms of the identification of their compartments as well as chemical features and alterations induced by disease. The aim of this work was to assess if higher magnification of optics in the FTIR microscope coupled with the focal plane detector (FPA) resulted in better resolution of lung structures and if the histopathological features correlated with clustering of spectral images. FTIR spectroscopic imaging was performed on paraffinized lung tissue sections from mice with optics providing a total magnification of 61Ã and 36Ã. Then, IR images were subjected to unsupervised cluster analysis and, subsequently, cluster maps were compared with hematoxylin and eosin staining of the same tissue section. Based on these results, we observed minute features such as cellular compartments in single alveoli and bronchiole, blood cells and megakaryocytes in a vessel as well as atelectasis of the lung. In the case of the latter, differences in composition were also noted between the tissue from the non-cancerous and cancerous specimen. This study demonstrated the ability of high-definition FTIR imaging to evaluate the chemical features of well-resolved lung structures that could complement the histological examination widely used in animal models of disease.