Double-stranded RNA (dsRNA), a hallmark viral material that activates antiviral interferon (IFN) responses, can appear in human cells also in the absence of viruses. We identify phosphorothioate DNAs (PS DNAs) as triggers of such endogenous dsRNAs (endo-dsRNAs). PS DNAs inhibit decay of nuclear RNAs and induce endo-dsRNA via accumulation of Intronic and Intergenic Inverted Retroelements (IIIR). IIIRs activate responses distinct from the antiviral response and do not turn on transcriptional RIG-I/MDA5/IFN signaling, but trigger the dsRNA-sensing pathways of OAS3/RNase L and PKR. The RNase L pathway acts both as a sensor and a cleavage system for these classes of RNAs. Thus, our data suggest that nuclear RNA decay and nuclear-cytosolic RNA sorting provide a checkpoint controlling innate immune response to human endo-dsRNAs. OAS3/RNase L and PKR form a specialized arm of the innate immune system, distinct from antiviral IFN signaling, which monitors quality of RNA sorting by sensing escaping IIIRs.