Most organisms have multiple forms of RNase H; two RNases H that are dissimilar in primary amino acid sequence yet have similar structural and, presumably, a common enzymatic mechanism. To address the cellular roles of these RNases H, we have examined the effects of eliminating RNases H in unicellular organisms such as bacteria and fungi. We have developed several mouse lines that are permitting us to see in detail the role for RNase H1 in replication of mitochondrial DNA. Patients with mutated RNase H1 exhibit typical muscular defects observed in other mitochondrial-related disease. Severe neuroinflammatory issues are seen in Aicardi-Goutieres Syndrome caused my defects in RNase H2. Major substrates for RNases H for RNases H are RNA/DNA hybrids that form during transcription. Failure to resolve these R-loops can have wide-spread effects that can lead to genome instability.