Pluripotent stem cells (PSCs) hold great promise in cell-based therapy, but the genomic instability seen in culture hampers their full application. A greater understanding of the factors that regulate genomic stability in PSCs could help address this issue. Here we describe the identification of Filia as a specific regulator of genomic stability in mouse embryonic stem cells (ESCs). Filia expression is induced by genotoxic stress. Filia promotes centrosome integrity and regulates the DNA damage response (DDR) through multiple pathways, including DDR signaling, cell-cycle checkpoints and damage repair, ESC differentiation, and apoptosis. Filia depletion causes ESC genomic instability, induces resistance to apoptosis, and promotes malignant transformation. As part of its role in DDR, Filia interacts with PARP1 and stimulates its enzymatic activity. Filia also constitutively resides on centrosomes and translocates to DNA damage sites and mitochondria, consistent with its multifaceted roles in regulating centrosome integrity, damage repair, and apoptosis. Display omitted •Loss of Filia promotes genomic instability and transformation in ESCs•Filia is induced by genotoxic stress and regulates repair responses•Filia is regulated by post-translational modification and sub-cellular translocation•Filia interacts with PARP1 and stimulates its enzymatic activity Zhao et al. identify Filia as an ESC-specific regulator of genomic stability that is induced by genotoxic stress. Functional characterization highlights dynamic subcellular translocation and roles in governing multiple DNA damage response pathways, including stimulation of PARP1 enzymatic activity.