In this study, Zezulin et al. describe the essential role of transcription factor RUNX1 in controlling the inflammatory transcriptional program in granulocyte–monocyte progenitors and neutrophils. The loss of RUNX1 causes derepression of TLR4 and type I IFN signaling pathways and retroelements, resulting in neutrophil hyperresponsiveness and innate immunity disorders or malignancies.