The Epstein-Barr virus (EBV), a human herpesvirus that is predominantly latent after infection, can be induced to replicate by deleted, rearranged EBV DNA from cultures of laboratory strain P3HR-1. Because mucosal surfaces are permissive of EBV replication, 101 oral biopsies from 70 Chinese and 5 American patients were examined for natural counterparts to tissue culture defective virus (WZhet), using as marker the abnormal juxtaposition of BamHI W and Z EBV DNA restriction fragments. Of the 49 oral biopsies that contained EBV DNA, 12 (24%) had the rearranged WZ fragment by polymerase chain reaction analysis: 3 (42%) of 7 EBV-positive epithelial dysplasias or carcinomas, 6 (38%) of 16 hairy leukoplakias, and 3 (12%) of 25 nonmalignant salivary gland biopsies. Accompanying viral replication was confirmed by in situ cytohybridization and demonstration of the linear configuration of the genome in select WZhet-positive lesions. These findings indicate that defective EBV with the unusual property of disrupting EBV latency is prevalent in natural infections and may contribute to EBV's pathogenic diversity.