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The integration of high-risk human papillomavirus (HPV) into host cell genome is one of the major contributing factors to cervical malignant transformation. The detection of HPV integration is helpful for understanding its role in cervical carcinogenesis and tumor progression. However, there is no ideal detection method of HPV physical status for clinical use. The study was to explore an ideal method of detecting the physical status of HPV-16.Setting HPV-16 plasmid as standard, multiplex real-time polymerase chain reaction (PCR) using 2 different fluorescent report radicals was used to quantify the copy numbers of E2 and E6 genes for analysis of the physical status of HPV-16 according to E2/E6. Multiplex real-time PCR test and Southern blot results of cervical cancer cell line SiHa and 27 specimens of HPV-16-positive cervical squamous cell carcinoma were compared.There was a linear relationship between the threshold cycle values and the copy numbers of E2 and E6 in both standard curves, with the correlation coefficients of 1.00 and the amplification efficiencies of above 95%. The 95% reference range of plasmid E2/E6 ratio, in which the amount of E2 DNA was equal to that of E6 DNA, was 0.81-1.29. The cut-off value of E2/E6, which was used to distinguish the pure episomal form from a mixed form of episomal and integrated HPV-16, was 0.81 in the multiplex real-time PCR test. HPV-16 was observed to be integrated into the host genome of SiHa cells by multiplex real-time PCR and Southern blot. The coincidence rate of multiplex real-time PCR and Southern blot was 81.5% (22/27) in the cervical squamous cell cancer tissues (kappa=0.844, P0.001).Multiplex real-time PCR test is a rapid, sensitive and reliable method for detecting the physical status of HPV-16 DNA, and is convenient to be applied in paraffin-embedded tissue and small preneoplastic or early neoplastic cervical lesions, even in cervical scrapes which contain a small amount of DNA.