The intestinal epithelium harbors stem cells at the bottom of crypts. Intestinal stem cells(ISCs)differentiate toward two alternative lineages of secretory or absorptive cells in a unidirectional manner. Studies have revealed factors that are indispensable for maintaining proliferation and differentiation of ISCs, which are provided from the surrounding environment. Additionally, several back-up systems compensating the sudden and massive loss of the ISC pool has been reported. Recent development of the three-dimensional culture system of ISCs in vitro has greatly contributed to elucidate these functional analyses of ISCs.