Exposure to high levels of ionizing radiation (IR) (>0.5 Gy) negatively affects health, but less is known about the effects of low-dose ionizing radiation (LDIR). Recent evidence suggests that it may have profound effects on cellular functions. People are commonly exposed to LDIR over natural background levels from numerous sources, including LDIR from medical diagnosis and therapy, air travel, illegal IR waste dumpsites, and occupational exposures in the nuclear and medical sectors. Stem cells reside for long periods of time in our bodies, and this increases the possibility that they may accumulate genotoxic damage derived from extrinsic LDIR or intrinsic sources (such as DNA replication). In this review, we provide an overview of LDIR effects on the biology of stem cell compartments. The principal findings and issues reported in the scientific literature are discussed in order to present the current understanding of the LDIR exposure risk and assess whether it may impact human health. We first consider the general biological consequences of LDIR exposure. Following this, we discuss the effects of LDIR on stem cells as discovered through in vitro and in vivo studies. Stem Cells 2018;36:1146-1153.