Whole genome sequences for three Epstein-Barr virus strains (B95-8, GD1 and AG876) were aligned and compared. In addition to known variable loci (including type-specific alleles for the EBNA2, EBNA3A, EBNA3B and EBNA3C genes, plus the EBNA1 and LMP1 genes), seven large-scale regions of lower-level diversity were identified with strains at each in two major groupings. All three possible patterns of strain associations were represented across the seven loci. Tree-building studies supported the existence of two distinct lineages in each case, and occurrence of recombination between lineages therefore has to be invoked to account for the observed genotypes of virus strains.