The intrinsic anatomical complexity of the lung, its slow cell turnover, and the lack of regenerative models are among the factors that have complicated the study and isolation of adult lung stem cells. Despite this, several endogenous lung progenitor cells have been identified in the proximal and distal lung. However, there is limited data regarding the lineage relationships, self-renewal properties, and clonality of these specific lung cell progenitors. More recent work showing that marrow cells can engraft as differentiated cells of solid organs has suggested new stem cell paradigms for the lung. In this review, we explore the implications of these new studies for lung stem cell biology. We also summarize and discuss the ongoing controversies that these studies have generated.