The prevalence of the Epstein-Barr virus (EBV) Taiwan variant was investigated in the throat washing (TW) samples from patients with head and neck tumors, persons with nonmalignant diseases, and healthy adults in Taiwan. By using the EBV (BNLF-1 gene)-specific primers and PCR, the EBV latent membrane protein gene BNLF-1 was detected in 91 (61%) of the 150 TW samples from patients with tumors, including 25 (78%) of 32 patients with nasopharyngeal carcinoma and 66 (56%) of 118 other patients with head and neck tumors. The TW samples from the 26 patients with nonmalignant tumors and 53 healthy adults were also examined. Approximately 47% of these samples were positive for the EBV gene. The PCR products of the BNLF-1 gene were then subjected to XhoI digestion. Sixty-eight of 91 PCR products (75%) showed the loss of the XhoI site, which indicated the presence of a Taiwan strain of EBV in patients with tumors. The DNA sequence of the BNLF-1 gene of the Taiwan variant revealed that the loss of the XhoI site was due to a nucleotide change from a G to a T at position 169,426 in comparison with the sequence of prototype EBV B95-8 cells. Furthermore, the Taiwan strain appeared significantly more frequently in the TWs and tissue samples from patients with nasopharyngeal carcinoma (88%; P < 0.001) and laryngeal carcinoma (80%; P < 0.02) than in those samples from healthy adults (about 40%). These data indicate that a Taiwan variant of EBV may be closely associated with head and neck tumors and suggest that this variant may be important in the pathogenesis of head and neck tumors.