The small intestine epithelium undergoes rapid and continuous regeneration supported by crypt intestinal stem cells (ISCs). Bmi1 and Lgr5 have been independently identified to mark long-lived multipotent ISCs by lineage tracing in mice; however, the functional distinctions between these two populations remain undefined. Here, we demonstrate that Bmi1 and Lgr5 mark two functionally distinct ISCs in vivo. Lgr5 marks mitotically active ISCs that exhibit exquisite sensitivity to canonical Wnt modulation, contribute robustly to homeostatic regeneration, and are quantitatively ablated by irradiation. In contrast, Bmi1 marks quiescent ISCs that are insensitive to Wnt perturbations, contribute weakly to homeostatic regeneration, and are resistant to high-dose radiation injury. After irradiation, however, the normally quiescent Bmi1 + ISCs dramatically proliferate to clonally repopulate multiple contiguous crypts and villi. Clonogenic culture of isolated single Bmi1 + ISCs yields long-lived self-renewing spheroids of intestinal epithelium that produce Lgr5-expressing cells, thereby establishing a lineage relationship between these two populations in vitro. Taken together, these data provide direct evidence that Bmi1 marks quiescent, injury-inducible reserve ISCs that exhibit striking functional distinctions from Lgr5 + ISCs and support a model whereby distinct ISC populations facilitate homeostatic vs. injury-induced regeneration.R-spondin | Dickkopf-1 | intestinal regeneration T he G protein-coupled receptor Lgr5 and the Polycomb group protein Bmi1 are two recently described molecular markers of self-renewing and multipotent adult stem cell populations residing in the crypt of the small intestine, capable of supporting regeneration of the intestinal epithelium (1, 2). Despite their similar ability to functionally repopulate the intestinal epithelium as demonstrated by independent in vivo lineage tracing experiments in reporter mice, the intestinal stem cells (ISCs) identified by these two molecular markers are spatially distinct. Whereas Lgr5 + ISCs are crypt base columnar (CBC) cells (1, 3) interspersed between Paneth cells and expressed throughout the intestine, Bmi1 + ISCs are mostly restricted to the "+4" cell position abutting the uppermost Paneth cell in proximal small intestine crypts (2). Lgr5 + ISCs are actively cycling (1), equipotent, and contribute to intestinal homeostasis by neutral drift competition (4-6). By comparison, Bmi1 + ISCs are less well characterized, and because of the lack of direct evidence, their cell cycle status is variably ascribed to be rapidly (7) vs. slowly cycling (8). It has been suggested that Bmi1 and Lgr5 mark an overlapping and possibly identical or redundant population of ISCs (5, 7, 9); however, no direct exploration of their functional similarities and differences has been performed. Further, it is unknown how Bmi1 + and Lgr5 + ISCs relate to a proposed model in which the intestine differentially uses an actively cycling ISC population during homeostasis and a distinct quiesce...