Tissues have the capacity to maintain a homeostatic balance between wear-and-tear and regeneration. Repair of non-lethal injury also activates cell proliferation to repopulate the injured sites with appropriate cell types and to restore function. Although controversial, the source of the material appears to be at least partly from pools of unique, multipotent stem cells that reside in specialized locations referred to as "niches." Molecular interactions between the niche and the intracellular factors within stem cells are crucial in maintaining stem cell functions, particularly the balance between self-renewal and differentiation. Many of the mediators of the stem cell-niche interactions are similar or identical to those that control developmental pathways during organogenesis. In this review, we present a systematic discussion and evaluation of the relevant literature with a focused emphasis on three primary signaling pathways, WNT, SHH and BMP with potentially overlapping roles during both development and stem cell maintenance.