Endogenous double-stranded RNA (dsRNA) is intricately regulated in mammals to prevent aberrant activation of host inflammatory pathways by cytosolic dsRNA binding proteins. We define the endogenous dsRNA repertoire in mouse BMDMs during the inflammatory response to bacterial lipopolysaccharide. Editing by adenosine deaminases that act of RNA (ADAR) enzymes was quantified temporally using RNA-Seq data from activated mouse macrophages to identify 342 Editing Enriched Regions (EERs), indicative of highly structured dsRNA. Nearly all mouse EERs were present in 3’UTRs. A comparison of EERs from mouse and human revealed significant conservation of EERs between mouse EER- associated genes and homologous human genes. In addition, using publicly available data and experimental validation, a significant proportion of EERs were shown to accumulate in the nucleus, a strategy that is thought to prevent aberrant activation of proinflammatory cascades in the cytoplasm. Finally, the significant conservation of EERs and the enhancement of structured regions in human suggests an increasingly important role for these regions in human biology. Overall design: RNA-Seq of total RNA and immunoprecipitated dsRNA isolated from bone marrow-derived macrophages from C57BL/6 mice after activation with bacterial lipopolysacharide for 0, 6, or 12 hours.