Epstein-Barr virus (EBV) is known to be associated with two malignant diseases, nasopharyngeal carcinoma (NPC) and endemic Burkitt's lymphoma. In this study, the genomes of EBV in biopsy specimens from 4 NPC patients in Japan were analyzed using Southern blot hybridization. The NPC tissues of all examined cases contained rearranged EBV genomes whose BamHI H fragments were larger than those of prototype EBV genomes. One of them had a BamHI fragment containing contiguous sequences of BamHI Y and H. A single-sized EBV DNA terminus was observed in these NPC tissues, implying the evolution of the carcinoma from a single EBV-infected cell.