DNA mismatch repair (MMR) deficiency is the hallmark of Lynch syndrome (LS), an autosomal inherited predisposition for an early onset of colorectal cancer (CRC) characterized by the presence of high levels of microsatellite instability. CRC cell lines carrying a MMR gene mutation show higher mutation rates than MMR-proficient cells not only at microsatellites but also at telomeres. Here, the MMR protein MSH2 was downregulated in WI38 cells using an shRNA and stable clones were grown in a 5% O2 environment to reduce the effect of oxidative stress on the telomere shortening rate (TSR). It was found that clones with a greater than 60% protein downregulation had a higher TSR with an exponential relationship between protein content and TSR for the B but not the _ allele for 12q what might be related with the telomeric variant repeat structure. Additionally, oxidative stress was found to have a synergistic effect on TSR together with MMR deficiency. Mutant XpYp telomeres generated from LoVo (MSH2–/–) were studied by telomere variant repeat (TVR) analysis to understand the mutation process and a tendency towards deletions was suggested. Furthermore, a novel 3rd next generation sequencing technology was tested to obtain full information of the telomere repeat array establishing the bases for future experiments. Finally, telomere length was measured in saliva DNA from 37 controls and 91 LS patients. It was found that telomeres shortened with age at similar rates in both cohorts and no significant relationship was found between telomere length and age for MLH1+/– patients. Besides, MSH2+/– patients had significantly shorter age-adjusted telomere length for XpYp but not 12q than MMR+/+ and parent-children pair comparisons for age-adjusted telomere lengths showed that MMR+/+ children had longer telomeres than their MMR+/– siblings and their MMR+/– parent but shorter than their MMR+/+ parent.