The association of Epstein Barr virus (EBV) with Sjögren's syndrome (SS) is still in dispute. This study is aimed to investigate the existence of EBV genomes and their products in salivary glands of SS. Salivary gland samples were surgically obtained from Chinese patients. EBV DNA was detected in three of seven cases by dot blot hybridization and in four of seven cases by in situ hybridization. The EBV-encoded small RNA-1 (EBER1) was detected in two of seven cases by in situ hybridization. The immunohistochemical staining of EBV proteins showed that the EBV latent membrane protein-1 was detected in four of seven cases and that BZLF1, BALF2, and gp350/220 proteins associating with virus production were not expressed. In eight controls, no positive signal was observed by these methods. DNA in situ hybridization identified ERV on both epithelial cells and lymphocytes. On the other hand, EBER1-positive signals were exclusively localized on lymphocytes. These results indicate that two forms of EBV infection may exist in salivary glands of SS. One is EBER1-positive latency in lymphocytes, the other is EBER1-negative latency in epithelial cells. Frequent EBV detection in salivary glands of SS suggests that EBV plays a role in the genesis of SS.