Defects in DNA mismatch repair (MMR) are the molecular basis of certain cancers, including hematological malignancies. The defects are often caused by mutations in coding regions of MMR genes or promoter methylation of the genes. However, in many cases, despite that a hypermutable phenotype is detected in a patient, no mutations/hypermethylations of MMR genes can be detected. We report here a novel mechanism that a mutation in the MLH1 3-untranslated region (3-UTR) leads to MMR deficiency. A relapsed leukemia patient displayed microsatellite instability, but no genetic and epigenetic alterations in key MMR genes were identifiable. Instead, a 3-nucleotide (TTC) deletion in the MLH1 3-UTR was found in the patient's blood sample. The mutant MLH1 3-UTR was found to significantly reduce the expressions of both a firefly luciferase reporter gene and an ectopic MLH1 gene in model cell lines. Consistent with these observations, a significant reduction in the steady-state level of MLH1 mRNA was observed in white blood cells of the patient. These findings suggest that the mutant MLH1 3-UTR can cause a severely reduced/defective MMR activity conferring leukemia relapse, likely by down-regulating MLH1 expression at the mRNA level. Although the exact mechanism by which the mutant 3-UTR down-regulates the MLH1 mRNA is not known, our findings provide a novel marker for cancers with MMR defects.Genetic instability is considered both a hallmark of cancer and a pre-disposing condition that can lead to cancer. Multiple cellular mechanisms exist to prevent genetic instability, including a highly complex DNA damage response network and several DNA repair pathways. DNA mismatch repair (MMR) 2 is an important genome maintenance system, the primary role of which is to correct mismatches generated during DNA replication, homologous recombination, and DNA repair. The MMR system relies on the highly conserved MutS homolog (MSH) and MutL homolog (MLH) proteins for its function. In humans, at least three MSH genes (MSH2, MSH3, and MSH6) and four MLH genes (MLH1, MLH3, PMS1, and PMS2) have been identified. The MSH gene products form the MSH2-MSH6 (also called MutS␣) and MSH2-MSH3 (MutS) heterodimers, whereas the MLH gene products constitute heterodimers of MLH1-PMS2 (MutL␣), MLH1-PMS1 (MutL), and MLH1-MLH3 (MutL␥) (1). The importance of MMR in maintaining genomic stability is underscored by the fact that defects in this system are the genetic basis of certain types of hereditary and sporadic human cancers, including hereditary non-polyposis colorectal cancer (HNPCC) (1-4).Interestingly, despite that all above MSH and MLH genes are implicated in MMR, almost all MMR deficient cancers are associated with alterations in MSH2 and MLH1 (2-4) characterized by either genetic mutations in these genes or hypermethylation of the MLH1 promoter, which epigenetically silences the MLH1 expression (1). The selectively targeting on MSH2 and MLH1 for alterations in HNPCC and other MMR deficient cancers appears to be consistent with the fact MSH2 or MLH1 i...