Ribonuclease H2 (RNase H2) belongs to the family of RNase H enzymes, which process RNA/DNA hybrids. Apart from cleaving the RNA moiety of a plain RNA/DNA hybrid, RNase H2 participates in the removal of single ribonucleotides embedded in a DNA duplex. Mutations in RNase H2 lead to the chronic inflammatory disorder Aicardi-Goutières syndrome (AGS), which has significant phenotypic overlaps with the autoimmune disease systemic lupus erythematosus. RNase H2 knock-out mice are embryonic lethal. Mouse embryos lacking RNase H2 accumulate DNA damage and exhibit a p53-mediated growth arrest commencing at gastrulation. On a molecular level, the knock-out mice reveal that RNase H2 represents an essential DNA repair enzyme, whose main cellular function is the removal of accidentally misincorporated ribonucleotides from genomic DNA. Ribonucleotides strongly accumulate within the genomic DNA of RNase H2-deficient cells, in turn resulting in a massive build-up of DNA damage in these cells. The DNA lesions that arise from misincorporated ribonucleotides constitute the by far most frequent type of naturally occurring DNA damage. AGS-causing mutations have also been found in the genes of the 3'-exonuclease TREX1, the dNTP triphosphatase SAMHD1, as well as the RNA-editing enzyme ADAR1, defining defects in nucleic acid metabolism pathways as a common hallmark of AGS pathology. However, recent evidence gathered from RNase H2 knock-out mice might provide additional insight into the molecular mechanisms underlying AGS development and a potential role of DNA damage as a trigger of autoimmunity is discussed.