We have previously reported that doublecortin-like kinase 1 (Dclk1) is a putative intestinal stem cell (ISC) marker. In this report, we evaluated the use of Dclk1 as a marker of surviving ISCs in response to treatment with high-dose total body irradiation (TBI). Both apoptotic and mitotic Dclk1+ cells were observed 24 h post TBI associated with a corresponding loss of intestinal crypts observed at 84 h post TBI. Although the Notch signaling pathway plays an important role in regulating proliferation and lineage commitment within the intestine, its role in ISC function in response to severe genotoxic injury is not yet fully understood. We employed the microcolony assay to functionally assess the effects of Notch inhibition with DAPT on intestinal crypt stem cell survival following severe (> 8 Gy) radiation injury. We observed a nearly 50% reduction in the number of surviving Dclk1+ crypt epithelial cells at 24 h after TBI and similar reduction in the number of surviving small intestinal crypts at 84 h following pre-treatment with DAPT compared to radiation alone. These data demonstrate that inhibition of Notch signaling decreases ISC survival following radiation injury, suggesting that the Notch signaling pathway plays an important role in ISC mediated crypt regeneration. These results also suggest that crypt epithelial cell Dclk1 expression can be used as a surrogate marker to evaluate the early survival of ISCs following severe radiation injury.