Extensive molecular studies in development of the squamous cell carcinoma of larynx (SCCL) indicated the involvement of a variety of genes including the MLH1. To search for possible mechanism leading to MLH1 silencing in SCCL we studied LOH and promoter methylation in a homogeneous set of 62 larynx cancers. Then we evaluated immunohistochemically the MLH1 expression for 51 tumor specimens. Further, the results were correlated with microsatellite instability and subsequently with the clinical course of the disease. LOH at the MLH1 locus and aberrant methylation of its promoter were found in 47.9 and in 22.6% of tumors, respectively. A decreased expression was observed in 27.5% of the cases. MSI analysis of tumor DNA showed a microsatellite stable phenotype in 59 cases (95.2%). From our study it can be concluded that: i) molecular alterations of MLH1 play an important role in SSCL development, ii) both LOH and aberrant methylation contribute to the MLH1 inactivation in SCCL and are associated with a less advanced stage of differentiation of larynx tumors, iii) MLH1 inactivation does not lead to MSI in larynx cancer and MSI may not contribute to the development of SCCL.