To evaluate the significance and mechanism of microsatellite instability (MSI) in laryngeal squamous cell carcinoma (LSCC).We investigated the expression frequency and clinical significance of MSI in 50 LSCC patients. The status of MSI was evaluated by using microdissection, polymerase chain reaction, single-strand length polymorphism, and silver staining. Five markers on chromosomes 1p, 3p, 5q, 9p, and 17p were used. Two of the six components of mismatch repair (MMR)-hMLH1 and hMSH2-were investigated by an immunohistochemical approach.The informative case numbers of the five markers (D17S796, D3S3544, D5S656, D1S375, D9S162) were 44, 42, 45, 44, and 40 in all 50 cases, respectively. The incidence of MSI on D17S796 (TP53) was 20.5% (9 of 44), on D3S3544 (FHIT) was 14.3% (6 of 42), on D5S656 (APC) was 31.1% (14 of 45), on D1S375 (BCAR3) was 20.5% (9 of 44), and on D9S162 (CDKN2A) was 15.0% (6 of 40). Although there was no relationship between MSI status and age, gender, smoking history, tumour location, tumour differentiation, and T stage (p > .05), there was a strong relationship between MSI and relapse condition (p < .01). Also, MSI status correlated with MMR expression to some degree (p < .01). But it was common that negative and positive staining of MMR coexisted on the same slide.MSI and abnormal MMR may contribute to the carcinogenesis of a subset of LSCC. MSI may be a characteristic signal of tumour recurrence.