The adult mammalian lung is a beautifully complex, integrated system of numerous types of epithelial cells, supporting cells and matrix that synergize to make gas exchange possible. Recent identification of putative endogenous and extrinsic lung stem cell populations has added to the diversity of the respiratory system. Despite these new studies and data from years of analyses of lung injury models, careful cellular and molecular analyses are needed to further define the stem and differentiated cells in the pulmonary system. New tools enabling lineage tracing or transplantation in adult lung as well as understanding the key microenvironmental clues that control the response to lung injury will be important to advance the field of lung stem cell biology.