A variety of lung diseases, such as pulmonary emphysema and idiopathic pulmonary fibrosis, develop in the lung alveoli. Multiple cell types are localized in the alveoli, including epithelial, mesenchymal, and endothelial cells. These resident cells participate in the pathogenesis of lung disease in various ways. To elaborate clearly on the mechanisms of these pathologic processes, cell type-specific analyses of lung disease are required. However, no method exists for individually isolating the different types of cells found in the alveoli. We report on the development of a FACS-based method for the direct isolation of individual cell types from the adult human distal lung. We obtained human lung tissue from lung resections, and prepared single-cell suspension. After depleting CD45-positive cells, a combination of antibodies against epithelial cell adhesion molecule (EpCAM), T1α, and vascular endothelial (VE)-cadherin as used to delineate alveolar cell types. Alveolar Type II cells were highly purified in the EpCAM(hi)/T1α(-) subset, whereas the EpCAM(+)/T1α(-/low) subset contained a mixed epithelial population consisting of alveolar Type I and bronchiolar epithelial cells. The EpCAM(-)/T1α(-) subset included both microvascular endothelial and mesenchymal cells, and these were separated by immunoreactivity to VE-cadherin. Lymphatic endothelial cells existed in the EpCAM(-)/T1α(hi) subset. Isolated cells were viable, and further cell culture studies could be performed. These results suggest that this novel method enables the isolation of different cellular components from normal and diseased lungs, and is capable of elucidating phenotypes specific to certain alveolar cell types indicative of lung disease.