To isolate side population cells from newborn mice small intestinal mucosa, and to investigate the feasibility of constructing the murine intestinal stem cell population by fluorescence activated cell sorting. Small intestine mucosa organoids of mice were isolated and dissociated into single cells. The side population cells were stained with Hoechst 33342 and propidium iodide, then sorted using fluorescence activated cell sorting. Total RNA and protein were purified from sorted fractions to detect Musashi-1 expressions by RT-PCR and Western-blotting. Single cell suspension from mouse small intestine mucosa contained a viable population of cells, which showed the side population phenotype and were sensitive to verapamil. These cells were enriched for Musashi-1 mRNA and MSI-1 protein expression. Results demonstrated that the side population fraction separated from mice intestinal mucosa is enriched for intestinal stem cells, the murine intestinal stem cell population can be successfully constructed with fluorescence activated cell sorting.