Human pluripotent stem cells(h PSCs) represent heterogeneous populations, including induced pluripotent stem cells(i PSCs), endogenous plastic somatic cells, and embryonic stem cells(ESCs). Human ESCs are derived from the inner cell mass of the blastocyst, and they are characterized by the abilities to self-renew indefinitely, and to give rise to all cell types of embryonic lineage(pluripotency) under the guidance of the appropriate chemical, mechanical and environmental cues. The combination of these critical features is unique to h ESCs, and set them apart from other human cells. The expectations are high to utilize h ESCs for treating injuries and degenerative diseases; for modeling of complex illnesses and development; for screening and testing of pharmacological products; and for examining toxicity, mutagenicity, teratogenicity, and potential carcinogenic effects of a variety of environmental factors, including ionizing radiation(IR). Exposures to genotoxic stresses, such as background IR, are unavoidable; moreover, IR is widely used in diagnostic and therapeutic procedures in medicine on a routine basis. One of the key outcomes of cell exposures to IR is the change in gene expression, which may underlie the ultimate h ESCs fate after such a stress. However, gaps in our knowledge about basic biology of h ESCs impose a serious limitation to fully realize the potential of h ESCs in practice. The purpose of this review is to examine the available evidence of alterations in gene expression in human pluripotent stem cells after genotoxic stress, and to discuss strategies for future research in this important area. Human pluripotent stem cells (h PSCs) represent heterogeneous populations, including induced pluripotent stem cells (i PSCs), endogenous plastic somatic cells, and embryonic stem cells (ESCs). Human ESCs are derived from the inner cell mass of the blastocyst, and they are characterized by the abilities to self-renew indefinitely, and to give rise to all cell types of embryonic lineage (pluripotency) under the guidance of the appropriate chemical, mechanical and environmental cues. The combination of these critical features is unique to h ESCs, for setting and testing of pharmacological products; and for examining toxicity, mutagenicity, teratogenicity, and potential carcinogenic effects of a variety of environmental factors, including ionizing radiation (IR). Exposures to genotoxic stresses, such as backg round IR, are unavoidable; moreover, IR is widely used in diagnostic and therapeutic procedures in medicine on a routine basis. One of the key outcomes of cell exposures to IR is the change in gene expression, which may underlie the ultimate h ESCs fate after Such, a stress. However, gaps in our knowledge about basic biology of h ESCs impose a serious limitation to fully realize the potential of h ESCs in practice. The purpose of this review is to examine the available evidence of alterations in gene expression in human pluripotent stem cells after genotoxic stress, and to discuss strategies for future research in this important area.