Bullous pemphigoid antigen-1 (BPA1) and alpha(6)beta(4)-integrin colocalize at the hemidesmosomes in basal-layer keratinocytes of normal squamous epithelia. The expression of these genes was analyzed during the process of tumor cell invasion and metastasis on frozen sections of head and neck biopsies, and the structural appearance of hemidesmosomes was analyzed by electron microscopy. Despite a diminution of hemidesmosomal structures as revealed by electron microscopy, gene expression of BPA1 and alpha(6)beta(4)-integrins was distinctly upregulated with the onset of invasive growth, demonstrated at the mRNA level by in situ hybridization. The upregulated gene expression extended to the entire proliferative zone of invasive tumors, including the tumor cells which have lost contact with the basement membrane and no longer display hemidesmosomes. The polarized localization of the BPA1 and alpha(6)beta(4) proteins to the basal aspect of the peripheral tumor cells was largely retained in invasive but nonmetastatic lesions, but was lost upon progression to metastatic growth of head and neck squamous cell carcinomas (SCC), in which pericellular staining extended into many tumor cell layers. The results of this study confirm that expression of BPA1 and alpha(6)beta(4)-integrins is elevated in carcinoma cells but is not directed to intact hemidesmosomes. Importantly, this loss of directed localization is an indicator of the capacity to metastasize.