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Microsatellite instability (MSI) testing is frequently used to screen patients for the early detection of Lynch syndrome, the most common hereditary colorectal cancer syndrome. MSI testing compares microsatellite repeat lengths in tumor DNA with those in matched normal tissue from the same patient. Therefore, precise sample identification is critical for obtaining reliable test results. The Penta-C and Penta-D pentanucleotide markers are widely used for sample identification in MSI testing. We investigated instability, defined as allelic mismatches or shifts, discordant fragment sizes, or the appearance of alleles in tumor DNA that were absent in the corresponding normal DNA, in the Penta-C and Penta-D loci across 2609 paired colorectal tumor and matched normal tissue or blood DNA samples. The allele sizes of both markers did not match in 0.3% of microsatellite-stable (MSS) and 12.3% of microsatellite instability-high (MSI-H) patients (p < 0.001, difference in proportions, 12.0% (95% CI, 8.9-15.1%)). Non-matching allele sizes in 12.3% of the MSI-H tumors suggest that other repeat markers may also be unstable and not suitable for sample identification in these tumors.