AIMS: To analyse the physical state of different human papillomavirus (HPV) DNAs in 55 intraepithelial and invasive HPV associated cervical neoplasms. METHODS: Restriction analysis, using a panel of five HPV type specific enzymes, was carried out for each sample; this was followed by Southern blot analysis. RESULTS: Six (25%) of 24 cervical intraepithelial neoplasms had integrated DNA of different HPV types. In contrast, integration was detected in 25 (81%) of 31 cervical carcinomas. Tumour samples revealed differences in the integration profile of HPV16 and the other HPV types. Six (26%) of 23 HPV16 associated cancers contained only episomal DNA. In contrast, all eight tumours containing HPV18, 31, or 35 revealed integrated DNA exclusively. CONCLUSIONS: The results suggest that in advanced cervical intraepithelial neoplasia lesions, a subset of lesions can be identified in which the viral genome is integrated and there is a greater risk of malignant progression. In addition, HPV16 DNA was not present in the integrated form in 26% of tumours, suggesting that integration and subsequent inactivation of the transcriptional regulator, E2, are not essential steps for the development of HPV16 associated carcinoma. In this respect, the behaviour of HPV16 associated tumours is different from HPV18, 31, and 35 associated tumours, where the viral genome is always present in the integrated form.