Recent studies have indicated that different patterns of latent viral gene expression were observed in a number of Epstein-Barr virus (EBV)-positive tumors. Among the latent viral genes, EBERs and EBNA1 genes are commonly expressed in EBV-associated tumor cells. Out of eight EBERs-negative NPC cases, four were shown to be EBV DNA-positive by in situ PCR which could detect one copy of integrated EBV genome per cell. EBER1-expressing cells in paraffin-embedded sections of T-cell lymphoma cases were detected in about 44% of T-cell lymphoma cases while 66% of the cases showed positive for EBNA1 mRNA by in situ hybridization (ISH) with EBNA1 specific RNA probe, indicating the presence of T-cell lymphomas expressing EBNA1 mRNA but not EBER1. LMP1 mRNA was expressed in 53% of the cases which were strongly associated with aggressive clinical course. Thus, the introduction of DNA-RNA ISH for detection of EBNA1 mRNA and in situ PCR for detection of latent EBV DNA could provide a unique tool for the detection of latently infected cells in histological sections.