The inability to identify, isolate, and culture intestinal epithelial stem cells (IESCs) has been prohibitive to the study and therapeutic utilization of these cells. Using a Sox9^EGFP mouse model, we demonstrate that Sox9^EGFP fluorescence signatures can be used to differentiate between and enrich for progenitors (Sox9^EGFPsubLo) and multipotent IESCs (Sox9^EGFPlo). Sox9^EGFPlo cells generate “organoids” in a recently defined culture system that mimics the native IESC niche. These organoids possess all four differentiated cell types of the small intestine epithelium, demonstrating the multipotent capacity of Sox9^EGFPlo cells. Our results are consistent with the previously reported observation that single IESCs generate cryptlike units without a detectable mesenchymal cell component. A prospective search revealed that CD24 is expressed in the Sox9^EGFPlo population and marks IESCs that form organoids in culture. CD24 represents the first cell surface marker that facilitates fluorescence-activated cell sorting enrichment of IESCs with widely available antibodies without requiring a specialized fluorescent reporter gene mouse model.