In most nasopharyngeal carcinoma (NPC) biopsy specimens, the Epstein-Barr virus (EBV), particularly in the terminal repeat region genomic structure, reveals a clonal pattern. To evaluate this phenomenon in vitro, we infected EBV-negative NPC cell lines, which express secretory component (SC) protein on their cell surface, with EBV particles. The viral particles were obtained either from a subcloned single cell or from the original B95-8 cell line. EBV infection was performed by incubating IgA anti-EBV and EBV particles with NPC cells and confirmed by direct in situ PCR hybridization. Southern blot analysis of EBV terminal repeat in EBV-infected NPC cell lines was performed using a Xhol 1.9-kb DNA fragment from the right terminus of the EBV genome as a probe. We found that all four NPC cell lines (ie, NPC-TWO1; 03, 04, and 06) expressed SC protein on their surfaces and could be infected by EBV through the EBV IgA-SC complex. Southern blot analysis in the single cell-subcloned B95-8 cell line showed a clonal EBV terminal repeat with a higher molecular size; whereas the original B95-8 line revealed the polyclonal EBV DNA pattern. A similar clonal EBV genomic pattern with lower molecular size was seen in all EBV-infected NPC cell lines. For comparison, six NPC biopsy specimens were also examined; of these, five showed a single band, and the remaining showed one major band and several lower molecular-sized bands. The EBV genomic DNA in the infected cells was shown to be an episomal form. We conclude, therefore, that a single (clonal) form of EBV genome can be obtained from a mixed population of epithelial tumor cells, even when they are infected by multiple virions with single or multiple form(s) of the EBV genomic pattern.