Methyl cytosine (5mC) is highly susceptible to spontaneous deamination to a thymine, meaning this essential genomic regulator is also an endogenous mutagen. Repair of 5mC deamination must occur before DNA replication or the resulting CG>TG mutation will be passed on to daughter cells. Mbd4 is a glycosylase in the base excision repair (BER) pathway that identifies C:T mismatches in a CpG context and initiates repair. Mbd4 has previously been shown to be a critical safeguard against CG>TG mutations arising from methylation damage, however, it remains unclear which other repair processes are contributing. We have gone on to investigate other genes that have been implicated in 5mC damage repair, including Tdg (Thymine DNA glycosylase, another BER component) and Msh6 (a mismatch repair [MMR] pathway protein involved in identification of mismatches). We generated single and compound knockout mice and quantified the accumulation of spontaneous methylation damage in primary stem cell populations. Mice were aged to 3-6 months and single cell colonies grown from bone marrow or colon stem cells. We found that loss of Mbd4 resulted in an accumulation of an additional 1 CG>TG mutation per genome per day in both blood and colon stem cells. Loss of Tdg alone, or in combination with Mbd4, did not alter the mutation profile. Loss of Msh6 generates variable mutation loads among mice and we saw an increase in the number of CG>TG mutations ranging from 1-3 mutations/genome/day, however this was in the context of an overall increase in C>T mutations (1-6 mutations/genome/day) characteristic of a traditional MMR pathway defect. Combined loss of Mbd4 and Msh6 also produced a characteristic MMR signature. Our results suggest that Mbd4 may be acting as a stabilizing or recruitment factor in the MMR pathway.