Microsatellite instability (MSI) is a characteristic molecular phenotype of tumors from the hereditary nonpolyposis colorectal cancer (Lynch) syndrome. Routine MSI screening of tumors in patients is an efficient prescreening tool for the population-based detection of Lynch syndrome in the absence of family cancer history. We describe here the optimization of a denaturing high performance liquid chromatography (DHPLC) assay for MSI analysis with the "Bethesda" panel of markers recommended by the National Cancer institute and with a more recently proposed "pentaplex" panel of 5 mononucleotide repeat marker. By using various polymerase chain reaction primers and tumor DNA samples with known MSI status without the "stutter peaks" inherent in the capillary electrophoresis (CE) methods that are currently in use. Dilution experiments showed that the detection limit for MSI using DHPLC was atleast 1:100 thus avoiding the need for tumor enrichment by microdissection before analysis. Concordance between CE and DHPLC for the detection of instability in the Bethesda panel marker was 95%. Optimal DHPLC provides a sensitive and specific alternative for routing MSI analysis that is free of the stutter peaks observed with CE and which can be used with either the Bethesda or pentaplex mononucleotide marker panels.