Embedded ribonucleotides are the most common non-canonical nucleotides incorporated during replication, and the absence of cellular RNase H2 activity, which is essential for their removal, causes widespread genome instability and embryonic lethality in mice. We study the biological functions of RNase H2, the causes and consequences of embedded ribonucleotides, and their role in the autoinflammatory disorder Aicardi-Goutieres syndrome.