Whether particular Epstein-Barr virus (EBV) strains are preferentially selected in malignant diseases remains controversial. Assessment of the importance of strain variation in the pathogenicity of EBV has been hampered principally by the lack of accurate data on the prevalence of virus variants in the normal population. To clarify this issue, a detailed comparative analysis of the EBV genomes contained in normal nasal and nasopharyngeal mucosal tissues and in nasal T/NK-cell lymphoma, which originates at these anatomic sites, was carried out by PCR amplification across the 30-bp deletion and the 33-bp repeat loci in the LMP1 gene and the type-specific polymorphic loci in the EBNA2 and EBNA3C genes and by sequence analysis of the 3' C-terminal region of the LMP1 gene. Whilst the majority of EBV strains in either normal or tumour tissues were type 1 viruses with similar numbers of LMP1 repeats, a marked predominance of LMP1 deletion (del-LMP1) over non-deleted/wild-type LMP1 (wt-LMP1) variants was observed in nasal T/NK-cell lymphoma. Although del-LMP1 variants were also prevalent in the normal carriers of our population, wt-LMP1 was detected at a significantly higher frequency in normal vs. tumour tissues (p = 0.036). More critically, wt-LMP1 variants were found frequently in mixed infection with del-LMP1 variants in the normal carriers. Sequence analysis identified 2 major del-LMP1 (and several wt-LMP1) variants containing signatory nucleotide changes in relation to the prototype B95-8 sequence in both normal and neoplastic nasal tissues. Together, our data provide strong evidence for a selection mechanism for del-LMP1 over the wt-LMP1 variants in tumours.