To identify metastasis-associated molecules in oropharyngeal squamous cell carcinomas (OSCC), we recently compared mRNA expression profiles of cell lines derived from primary and metastatic lesions of OSCC using microarray technology. Cystatin M, an endogenous cathepsin B inhibitor, was expressed 40-fold higher in the metastatic versus the primary tumor cell line. To show that different cystatin expression levels affect the cell lines' sensitivities to TNF-induced apoptosis by differentially regulating cathepsin B activity. The 686Tu and 686Ln cell lines were established from a 49-year-old male patient with an OSCC involving the posterior tongue and oro-pharynx (tumor stage T(3)N(3B)). RT-PCR, Western blots, immunohistochemistry, and in situ hybridization all confirmed increased cystatin M expression in 686Ln compared to 686Tu cells, and in the parent archival tumors. TNF-alpha induced apoptosis was easily detected in 686Tu, but only marginally in 686Ln cells. Thus, we propose that elevated cystatin M expression aids metastasis by blocking intrinsic cathepsin B activity and rescuing tumor cells from TNF-induced apoptosis.