In order to compare nucleotide differences of Epstein-Barr virus (EBV) Bam HI F DNA fragment from various EBV associated diseases, polymerase chain reactions (PCR) were used to amplify a subfragment (nucleotides 55,381-56,020) of the F fragment from different tissue DNAs, including 20 NPCs, 2 B-cell lymphomas, 2 T-cell lymphomas, 3 infectious mononucleosis (IM), and 3 normal controls. DNA sequences were determined by PCR direct sequencing or sequencing after DNA cloning. The PCR products were cloned into pGEM-3Z vector, then the resulting recombinant plasmids were used to transform DH5 alpha competent cells. Plasmid DNAs from the correct transformants were prepared for DNA sequencing. The results showed that the proportion of the f variant in NPCs, B-cell lymphomas, T-cell lymphomas, IMs, and normals were 40%, 0%, 0%, 33%, and 33%, respectively. Because the f variant was not specifically more prevalent in NPC tissues compared to the non-tumor tissues, we speculate that there is no strong association between the f variant and NPC. These results were different from other reports. Coinfection of the F strain and the f variant was found both in some NPC patients and normal individuals. Analyses of Bam HI F subfragments of 35 EBV isolates from the 30 tissue DNAs revealed that there were changes at four corresponding positions of the B95-8 strain. They were nucleotide T at 55,473 replaced by G, an insertion of TGT after nucleotide 55,543, nucleotide A at 55,564 replaced by G, and nucleotide T at 55,958 replaced by C. These 4 nucleotide changes may confer a character of Taiwan strains. The nucleotides of the F strain at coordinates 55,519, 55,596, 55,680, 55,703, and 55,895 were T, T, A, A, and C, and those for the f variant were C, C, C, C, and T. These two patterns were not correlated with types A and B of EBV.