The adult stem cells, or tissue-specific stem cells, are essential for maintaining tissue homeostasis and commonly reside in specific local microenvironment named niche. The niche keeps stem cells in multipotent/unipotent state and prevents them from precocious differentiation, and in some cases, aligns them and promotes asymmetric division to produce differentiated progenies for tissue regeneration. The niches employ a variety of factors including cell adhesion molecules, extra cellular matrix, growth factors and cytokines in a tissue-specific manner to regulate the resident stem cells. Stem cells in turn may also contribute to niche integrity and function. Continuous elucidation of stem cell niche regulation at the cellular and molecular level would help understanding tissue homeostasis and disease mechanisms, and may also provide useful strategies for therapeutic application of stem cells.