The high rate of turnover of the intestinal epithelium is maintained by a group of stem cells which reside at the base of the crypts of Lieberkuhn. While the existence of these intestinal epithelial stem cells (IESCs) has been well established, their study has been limited due to the inability to isolate them. Previous work has utilized side population (SP) sorting of the murine small intestine to isolate a viable fraction of cells enriched for putative IESCs. In the present study, we have used gene expression profiling techniques to characterize the molecular features of this potential stem cell population. Further in situ hybridization (ISH) studies reveal that transcripts enriched in the SP tend to localize to the intestinal crypt base/progenitor cell zone, while de-enriched transcripts localize outside of this region. From a functional standpoint, gene ontology and pathway mapping analyses demonstrate that immune, mesenchymal and differentiated epithelial cells are depleted in the SP fraction, while putative progenitor cells are enriched in this cell population. Furthermore, the significance of the MODY pathway in these cells suggests that enteroendocrine progenitors are enriched in this cell fraction as well. In conclusion, SP-sorting of mouse small intestinal mucosa does appear to isolate cells with progenitor characteristics. These findings provide the foundation for membrane protein based sorting procedures that can be used to further fractionate these cells for transplantation experiments in the future.