Stem cells persist throughout life, replacing cells lost to homeostatic turnover, injury, and disease. However, their functions decline with age, which contributes to degeneration and dysfunction. The molecular mechanisms involved in the aging of stem cells are the same as the ones involved in the aging of somatic cells, including telomere shortening, oxidative stress, epigenetic dysregulation, miRNAs changes, alterations of DNA, RNA, proteome, and various cellular organelles. Aging impacts various pathways, such as insulin/insulin-like growth factor 1 (IGF-1), mTOR, FoxO, AMP-activated protein kinase (AMPK), sirtuin, and many others, resulting in senescent stem cells that exhibit functional and numerical impairment. Stem cells have developed special mechanisms to prevent age related damage accumulation and to sustain their stemness properties, however, these mechanisms lose their effectiveness over time. The most fatal consequence of this is found in the immune system, where both innate and adaptive immunity are affected, exhibiting a plethora of defects, including increased autoimmune disease occurrence, elevated tolerance to cancer and chronic inflammatory status. Stem cell therapies call for the best quality of stem cells grafts. Stem cell products should be devoid of cells containing a senescent phenotype, thus a comprehensive knowledge of the biology behind the senescence of stem cells should be taken into account in every cell based therapy.