Lymphoepithelioma of the nasopharynx is a neoplasm known to have a strong association with Epstein-Barr virus (EBV). Using the Southern blot method, polymerase chain reaction (PCR), and/or in situ hybridization, we examined lymph nodes containing metastatic carcinoma, including metastatic lymphoepithelioma, for the presence of EBV genomes in order to determine whether EBV was associated exclusively with lymphoepithelioma. All of six lymph nodes from patients with lymphoepithelioma in the neck were found to have EBV genomes using the above methods. In four of the six cases, the primary site was the nasopharynx, and in the other two no primary site was found. Four of 12 squamous cell carcinomas and one of 18 adenocarcinomas expressed the EBV genome only by PCR, but not by Southern blotting or in situ hybridization, probably due to the presence of latent EBV in lymphocytes. These results indicate that metastatic carcinoma in lymph nodes showing EBV genomes revealed by Southern blotting or in situ hybridization is lymphoepithelioma, and that the nasopharynx is very likely the primary site.