The ASCP designates this journal-based CME activity ("JMD 2017 CME Program in Molecular Diagnostics") for a maximum of 36 AMA PRA Category 1 Credit(s)ä. Physicians should claim only credit commensurate with the extent of their participation in the activity. CME Disclosures: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose. Colorectal (CRCs) and endometrioid (EMCs) cancers in patients with Lynch syndrome exhibit microsatellite instability (MSI) detected by PCR or immunohistochemistry (IHC). While both assays are equally sensitive for CRCs, some suggest that PCR has a higher false-negative rate than IHC in EMCs. We assessed the MSI profiles of 91 EMC and 311 CRC specimens using five mononucleotide repeat markers: BAT25, BAT26, NR21, NR24, and MONO27. EMCs with high MSI (MSI-H) showed a mean left shift of 3 nucleotides (nt), which was significantly different from 6 nt in CRCs. A shift of 1 nt was observed in multiple markers in 76% of MSI-H EMCs, whereas only 12% of MSI-H CRCs displayed a 1-nt shift in one of five markers. IHC against four mismatch repair proteins was performed in 78 EMCs. Loss of staining in one or more proteins was detected in 18 of 19 tumors that were MSI-H by PCR. When EMC tumor cell burden was diluted to <30%, MSI-H was no longer observed in two of three EMCs with a mean nucleotide shift of 1 nt. These results indicate that EMC and CRC MSI profiles are different and that caution should be exercised when interpreting the results, as subtle, 1-nt changes may be missed. These findings provide a potential cause of previously reported discordant MSI and IHC results in EMCs. Lynch syndrome (LS) (Online Mendelian Inheritance in Man no. 120435), also referred as hereditary nonpolyposis colorectal cancer, is an autosomal dominant disorder with a relatively common disease prevalence of 1 in 440.1,2 About 2% to 3% of colorectal cancers (CRCs) and 1% to 2% of endometrioid cancers (EMCs; including endometrial cancer and endometrioid cancer of the ovary) are due to LS.3 LS is a heterogeneous disorder exhibiting reduced penetrance, differences in age of onset, and variability in expression.In LS patients, the lifetime risks are 50% to 70% for CRC and 40% to 60% for EMC in women, and the overall risk for other associated tumors is increased. 4 LS is caused by germline mutations in one of four mismatch repair (MMR) genes or by a deletion in the EPCAM locus affecting the adjacent MMR gene.5 These germline mutations result in defective MMR machinery that leads to microsatellite instability (MSI) throughout the genome and gives rise to tumors. Both Lynch-related and sporadic cancers can manifest MSI. MSI tumors are associated with a better prognosis yet a poor response to adjuvant 5-fluorouracil based chemotherapy.