HLA class I antigen processing machinery plays a crucial role in the generation of peptides from endogeneously synthesized proteins and in their presentation to cytotoxic T lymphocytes. The purpose of this study was to analyze the downregulation of HLA class I antigen, transporter associated with antigen processing (TAP) and tapasin in primary and metastatic lesions of head and neck squamous cell carcinoma (HNSCC) and to compare TAP, tapasin and HLA class I antigen downregulation in metastatic lesions with that of primary lesions. We analyzed expression levels of TAP1, TAP2, tapasin and HLA class I antigen in 25 primary and autologous metastatic lesions by staining formalin-fixed, paraffin-embedded tissue sections in the immunoperoxidase reaction. We identified the expression levels of TAP1, TAP2, tapasin and HLA class I antigen were coordinately downregulated in both primary and metastatic lesions and were significantly lower in metastatic lesions than in autologous primary lesions tested. HLA class I antigen downregulation in metastatic lesion was significantly associated with reduced disease-free survival of patients (P<0.05). Multivariate Cox proportional hazards model analysis identified negativity of HLA class I antigen as an independent prognostic marker. HLA class I antigen and TAP are likely to be downregulated in metastatic lesions compared with primary lesions in HNSCC. The higher frequency of HLA class I antigen and TAP down-regulation in metastases play a role in the clinical course of the disease.