Human papillomavirus type 16 (HPV-16) is associated with neoplastic lesions of the uterine cervix. Viral transforming functions have been localized to the E6-E7 open reading frame (ORF) and this ORF is conserved consistently in cervical intraepithelial neoplasia (CIN). Two mRNAs, generated by alternative splicing, are expressed from the E6-E7 ORF. These are known as E6*I and E6*II, and potentially encode the viral E7 and E6 proteins, respectively. It is believed that the HPV-16 transforming ability is mediated by the E6 and E7 proteins. A quantitative RT-PCR assay, developed by us to characterize the relative expression of E6-E7 spliced transcripts, was applied to exfoliated cervical cells obtained from patients in varying stages of clinically defined CIN and who were infected with HPV-16. The relationship between viral expression, disease stage, oral contraceptive use and age was studied. No association was observed between age or oral contraceptive use and HPV-16 E6-E7 expression. However, when both E6*I and E6*II were detected, a direct correlation was observed between relative proportions of E6*I/E6*II mRNAs greater than 95%/5% and increased disease severity. This study underscores the importance of the relationship between quantities of viral transforming gene transcript and the course of cervical disease. It also suggests that quantification of HPV-16 E6-E7 transcription may be useful as a prognostic tool to identify women who are at increased risk of developing cervical cancer.