AIM: To examine the microsatellite instability (MSI) and loss of heterozygosity (LOH) in head and neck squamous cell carcinomas (HNSCC). METHODS: 36 cases of HNSCC were analyzed with 15 microsatellite markers from chromosome 3,5,6,8,9,13,17 and 18. RESULTS: Among the 36 cases of HNSCC, 27.8%(10/36)of samples showed MSI in one to eight microsatellite markers. High frequent MSI occurred at D17S520(22.9%), D6S105(16 7%)and D8S264(13 9%). LOH was detected on the site of 9p21-p22 and 3p14. No correlations were found between allelic instability and grade or stage of the tumor. CONCLUSION: Our data suggest that MSI is a common genetic change in HNSCC. Tumor suppressor genes related to HNSCC may harbor at chromosome 9p21-p22 and 3p14 regions. [