The prevalent strain of Epstein-Barr virus (EBV) in EBV-related malignancies and in healthy adults in Southern Japan was examined by means of polymerase chain reaction (PCR) and/or restriction fragment length polymorphism (RFLP) analysis. In EBV-related gastric cancers, 51/73 cases were subtype A, 4 were subtype B and the EBNA-2 region was not amplified in 18 cases. Sixty-three were wild-type F, and only one was variant "f". Sixty-one cases had type C and 2 type D. EBNA-2 subtype A was found in 10/12 EBV-related T/NK-cell lymphomas, and 11 samples harbored the wild-type F. Neither subtype B nor the "f" variant was detected. Type C EBV was found in 8 cases and type D in 3 specimens. Two Japanese nasopharyngeal carcinomas (NPC) harbored subtype A with wild-type F and type C. Throat washings from healthy adults harbored wild-type F virus in 60/153 cases, and 25 of these samples were EBNA-2 subtype A. Type C viruses were detected in 92% of cases and type D in 7.4%. Therefore, the prevalent strain in EBV-related malignancies in Southern Japan was the same as in the healthy population in this geographical region.