In order to investigate the relationship between Epstein-Barr virus (EBV) latent infection and histogenesis of odontogenic disorders, in situ hybridization for EBV-encoded small RNA (EBER) was applied to the paraffin sections of ameloblastoma, dentigerous cyst, and odontogenic keratocyst. Eight cases (15%) of 53 ameloblastomas showed scattered signals for EBER in the parenchymal cells, whereas no reaction of EBER transcript was observed in the non-neoplastic cystic lesions. In the ameloblastoma, the follicular and plexiform types revealed the signals in the nuclei, but cystic, acanthomatous, granular, and basal cell types exhibited no reaction with EBER. The distribution of the signals without monoclonarity indicated that ameloblastoma cells may exclude EBV genomes or inactivate EBER-encoded genes. The results suggested that EBV participates as one of the transforming factors in the occurrence of ameloblastoma.