A DNA fragment containing Epstein-Barr virus (EBV) terminal fragment sequence was obtained from a genomic library of nasopharyngeal carcinoma (NPC). One of the clones (clone 1510) contained the gene encoding latent membrane protein (LMP). Sequence analysis revealed that this gene had 95% homology with the LMP sequence of the B95-8 strain. Among the sequence variations, there was a change from G to T at nucleotide position 169,426, resulting in the loss of an XhoI site in exon 1 of the LMP gene. A pair of primers bracketing the XhoI site were designed to synthesize the EBV DNA fragment from nucleotides 169,081-169,577 by using the polymerase chain reaction (PCR) method. The PCR products were then subject to XhoI digestion and to DNA sequencing analysis. This restriction enzyme site polymorphism along with the sequence variations were also observed in 50 biopsy tissues as well as in the throat washings of 6 out of 20 healthy individuals that we examined, indicating that the EBV strain predominantly existing in these biopsy tissues was different from strains of B95-8, Jijoye or nude mouse passaged cells (C15) with an African origin, but closely resembled other nude mouse passaged CAO cells which were originally derived from China. Balb/c 3T3 cells carrying this NPC-LMP gene showed a transformed cell morphology and were tumorigenic in nude mice. The relationship between this unique type of EBV and NPC has yet to be established.