Multiplex PCR with specific primers for E2/E6 genes was used to assess the viral integration status of HPV-16 in women with low and high grade squamous intraepithelial lesions (LSIL and HSIL, respectively) in comparison to cervical cancer patients. Women with confirmed HPV-16 infection were examined: 30 with LSIL, 12 with HSIL and 23 with cervical cancer. The PCR products were separated electrophoretically in agarose gels and densitometric analysis was performed using Bio-Rad Quantity One software. E2 and E6 sequences of HPV-16 were detected in 91% of the women. The free episomal viral genome was not detected in the cervical carcinoma group. Twenty six percent of the samples obtained from this group harboured the integrated form, whereas the remaining samples possessed a mixture, i.e. episomal and integrated forms of viral DNA. The free episomal form dominated in women with LSIL and HSIL. In 6 cases the episomal and integrated forms were detected simultaneously. HPV-16 integration occurred in a subset of LSILs and HSILs, not only in the cervical cancer patients and correlated with progression of cytological changes. The assessment of the status of HPV-16 may be the molecular factor preceding the morphological features leading to malignancy.