The specification, maintenance, division and differentiation of stem cells are integral to the development and homeostasis of many tissues. These stem cells often live in specialized anatomical areas, called niches. While niches can be complex, most involve cell-cell interactions that are mediated by adherens junctions. A diverse array of functions have been attributed to adherens junctions in stem cell biology. These include physical anchoring to the niche, control of proliferation and division orientation, regulation of signaling cascades and of differentiation. In this review, a number of model stem cell systems that highlight various functions of adherens junctions are discussed. In addition, a summary of the current understanding of adherens junction function in mammalian tissues and embryonic and induced pluripotent stem cells is provided. This analysis demonstrates that the roles of adherens junctions are surprisingly varied and integrated with both the anatomy and the physiology of the tissue.