Integration of HPV genome into host chromosomes represents an early clonal event to provide an additional selective advantage for the expansion of the neoplasm. Viral transcripts have been detected by the APOT assay. Although APOT assay has some advantages in detection transcripts from each chromosome integration site, there are several limitations. First, it is difficult to amplify very long integration-derived transcripts, which will underestimate the number of tumors with integrated HPV DNA. Second, APOT is one type of nested PCR, which may tend to amplify the transcripts with higher levels and ignore those with lower levels. Third, It has been reported that the internal poly A priming could replace the oligo primer within certain limits, and generating a set of anchored oligo primers for cDNA synthesis. These sequences caused by internal priming interrupted the generating of full-length cDNA and confused the analysis of alternative splicing. With our modified APOT assay to detect the transcription pattern of the cervical tissues, we did find many viral transcripts connected with poly A or host genome sequences in HPV16-infected cervical squamous epithelial tissues. HPV16 transcription patterns in LSIL, HSIL, and CxCa were significantly different. We found that the Type C transcript was only detected in the samples of CxCa and more random integration sites existed in our tissue samples. Similar to previous reports, our study indicates that HPV integration has no preferential site in the human genome. Except for chromosome 21 and X, other chromosomes are all susceptible to HPV16 integration. Approximately 55% integrations are located in or close to a fragile site. Different from previous reports, we noticed that integration events often occur multiple times significantly more in cervical cancer than in LSIL and HSIL. These data not only provide biological support to the epidemiologic observation that persistent infection by specific types of HRHPV is the important cause of cervical carcinoma, but also indicate that subsequent selection for and accumulation of mutations in yet-to-be-identified key cellular regulatory genes promotes further progression to cervical cancer.