Many Sjögren's syndrome patients complain primarily of dry eye. Epstein-Barr virus DNA has recently been found in the lacrimal glands of Sjögren's syndrome sufferers and normal individuals, and lacrimal glands are thought to be a target organ for latent Epstein-Barr virus infection. In this study, we performed lacrimal and salivary gland biopsies on 9 Sjögren's syndrome patients. Extracted Epstein-Barr virus DNA was assayed by polymerase chain reaction and compared to that of healthy individuals. An increased level of Epstein-Barr virus DNA was observed in all of the lacrimal glands and 8 of the 9 salivary glands from the Sjögren's syndrome patients. However, the amount of genome in the lacrimal gland was more than 10 times that in the salivary glands, not only in the Sjögren's syndrome patients but also in the controls. This may explain the pathogenesis of dry eye in patients with Sjögren's syndrome, and why the lacrimal gland tends to be so prominently affected. It may also suggest a therapeutic approach for this and possibly other types of dry eye.