Background and Objectives: Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant cancer predisposition syndrome caused by germ-line mutations in DNA mismatch repair genes. Tumors arising as a result of these mutations display instability in a sequence area known as microsatellites. Studies have shown that some Bethesda markers (BAT25, BAT26) are more efficient than others in identifying Microsatellite Instability (MSI) in tumors of HNPCC patients. The aim of this study was toevaluate the possible benefits of two MSI markers BAT25 and BAT26 to identifying microsatellite instability in tumor tissues from HNPCC patients. Material & Methods: We used 49 cases gathered from north-east Iran. Microsatellite Instability analysis was performed using fluorescent-labeled primers. Statistical analysis was achieved using SPSS software. Results: 24/5% (12/49) and 34.7% (17/49) of the cases showed MSI in BAT25 and BAT26, respectively. None of tumor sample was MSI positive for both markers. Discussion: MSI frequency is considerably lower, compared to other findings. This might be due to the fact that environment and Race has great influence on MSI frequency.