Adult stem cells exist in most mammalian tissues to maintain their homeostasis and help repair them. Reductions in adult stem cell function and/or number are clearly associated with aging, however, the causal correlations between such findings and the effects of aging are largely unknown. Some stem cell functional changes, such as the loss of lineage specificity and self-renewal capacity, senescence and transformation, arise in stem cells autonomously during the aging process. These autonomous changes of stem cell functions reflect the damaging effects of age on the genome, epigenome, and proteome. Other stem cell functional changes are influenced by the age-related changes in the local microenvironments (niches) or systemic environments. If stem cell-based therapy can be used not only for age-related degenerative diseases, but also normal functional declines associated with aging, consideration of the behavior of stem cells based on effects from the local microenvironments (niches) and systemic environments in older individuals will therefore be needed.