AbstractTumors of Lynch syndrome (LS) patients display high levels of microsatellite instability (MSI), which results from complete loss of DNA mismatch repair (MMR), in line with Knudson’s two-hit hypothesis. Why some organs, in particular those of the gastrointestinal (GI) tract, are especially prone to tumorigenesis in LS remains unknown. We hypothesized that MMR is haploinsufficient in certain tissues, compromising microsatellite stability in a tissue-specific manner before tumorigenesis. Using mouse genetics, we tested how levels of MLH1, a central MMR protein, affect microsatellite stability in vivo and whether elevated MSI is detectable prior to loss of MMR function and to neoplastic growth. We assayed MSI by sensitive single-molecule PCR in normal jejunum and spleen of 4- and 12-month old Mlh1+/+, Mlh1+/− and Mlh1−/− mice, accompanied by measurements of Mlh1 mRNA and MLH1 protein expression levels.While spleen MLH1 levels of Mlh1+/− mice were, as expected, approximately 50% compared to wildtype mice, MLH1 levels in jejunum varied substantially between individual Mlh1+/− mice and decreased with age. Apparently, Mlh1+/− mice with soma-wide Mlh1 promoter methylation were the most venerable to MLH1 expression level decrease in jejunum. MLH1 levels (prior to complete loss of the protein) inversely correlated with MSI severity in Mlh1+/− jejunum, while in spleens of the same mice, MLH1 levels and microsatellites remained stable. Thus, Mlh1 haploinsufficiency affects specifically the intestine where MMR levels are particularly labile, inducing MSI in normal cells long before neoplasia. A similar mechanism likely also operates in the human GI epithelium, and could explain the wide range in age of onset of LS-associated tumorigenesis.