Transcription of the E6 and E7 viral oncogenes of human papillomavirus (HPV) type 16 is regulated by the P97 major early promoter, and enhancer and silencer elements found in the long control region (LCR). In this study, we tested the transcriptional activity of natural HPV 16 variants having long deletions in the LCR. The HPV 16 LCR regions were amplified from invasive cervical cancer specimens, and cloned into the reporter vector pALuc. Transcriptional activity of the different clones was measured by luciferase test after transient transfection into HeLa cells. The deletions found in the LCR encompassed parts of the enhancer and either the YY1-specific silencer alone or together with the CDP-specific silencer. The transcriptional activity of these deletion variants were usually reduced compared with that of the corresponding full-length clones. However, a deletion variant lacking the whole enhancer and both silencer regions retained substantial enhancer activity on the P97 promoter. These results point to the existence of a novel context-dependent enhancer element in the 5' LCR of HPV 16.