The conventional perception of HPV type 18 is that it is associated principally with invasive cancer of the cervix. However, in precursor lesions it is frequently identified in lesions of lower grade morphology, in contrast to the typical high grade lesions associated with HPV 16. To better characterize this uncommon relationship of low grade morphology and high risk virus, we studied four low grade and two high grade intraepithelial lesions of the cervix which were shown to contain HPV 18 by polymerase chain reaction/restriction fragment length polymorphism analysis. Immunohistochemistry and in situ hybridization identified capsid proteins and viral DNA in an epithelial distribution characteristic of episomal replication and late gene expression. Sequencing of the E2, E6, E7, and upstream regulatory regions revealed four silent mutations within these precursor lesions. Two of these sequence alterations were also noted in three of four HPV 18 positive squamous carcinomas, suggesting a viral subtype which was not unique to cervical precursors. The bland morphology of many HPV 18 related precursors contrasts with the high grade morphology of HPV 18 associated cancers. However, this diversity cannot be linked to functional differences in sequences encoding in vitro transforming potential, transcriptional regulation, or transactivation functions. Whether these differences in lesion phenotype relate to unique host variables remains to be determined.