Many diseases and/or physical defects due to injury result in the loss of specialized cells within organ systems and lead to organ system dysfunction. The ultimate goal of cell-based therapies is to regenerate and restore normal function. Populations of embryonic, fetal, adult stem cells and inducible pluripotent stem cells generated by reprogramming of adult cells show promise for the treatment of a variety of diseases. In addition, the recent advancements in adult stem cell biology in both normal and pathological conditions have led to the identification of some intrinsic and extrinsic factors that govern the decision between self renewal versus differentiation of tissue-resident adult stem cells. This is of primary importance for the design of an approach of stem cell-based therapy focused on their in vivo modulation by conventional chemical and biological therapeutics capable to stimulate endogenous cell regeneration. Such therapeutics can act in vivo to promote cell survival, proliferation, differentiation, reprogramming and homing of stem cells or can modulate their niches. In this review, we will highlight the burst of recent literature on novel perspectives of regenerative medicine and their possible clinical applications.