Two types of Epstein-Barr virus (EBV), EBV-1 and EBV-2, were identified on the basis of DNA sequence divergence in the genes for nuclear proteins EBNA 2, 3a, 3b and 3c. In the present study, we conducted an immunological and genomic analysis in a human immunodeficiency virus (HIV)-infected population to determine the prevalence of the two types, and whether the identified type was stable over years. The EBNA-2 serotyping and genotyping showed that HIV-infected patients were highly infected by EBV-2, and that the dominant strain was mostly retained. However, during a follow-up study, a change in the dominant viral strain was observed in two patients. A first HIV-positive patient (patient A), although having a stable level of anti-EBNA-2A and -2B antibodies, showed a change in the genotype and antigen produced in spontaneously established lymphoblastoid cell lines (LCL). The sequence analysis of LCLs confirmed the emergence of the EBV-2 type population. A strain from a second HIV-positive patient (patient B) was clearly identified as EBV-2: the genotype from a saliva sample and from sequential LCLs belonged to EBV-2, as well as the antigen produced from LCLs, and serum antibodies. After a 5-year continuous EBV-2 infection, a reactivation of the EBV-1 strain was observed. In both cases, sequence analysis of the EBNA-2 gene showed, only with EBV-1, the presence of EBV variants related to the B95-8 prototype. Two mutations (at nucleotides 49212 and 49304) were found in both patients A and B, whereas an additional mutation (at nucleotide 49237) was characteristic of the patient A. No mutation relative to the prototype B95-8 strain was observed in a subsequent analysis of this EBNA-2 region from LCLs obtained from two HIV-negative patients predominantly infected by EBV-1. Therefore, we speculate that these mutations may be EBV-1 mutations specifically occurring during HIV infection.