Background: Human papillomavirus (HPV) infection has been reported as an important cause of cervical cancer for many years. HPV16 and HPV18 are the two most prevalent types in cervical cancer5. Integration of HPV DNA is a crucial genetic event in cervical carcinogenesis. Therefore, it is important to know the HPV integration hot spots in human genome to predict the cervical cancer development status of patients. Although many studies have addressed the HPV integration sites in human genome, it is still a technique barrier to precisely determine the HPV integration sites of each patient, especially at early disease development stage with limited integration sites existing. Methods: To solve this problem, we first designed HPV probes to capture HPV integrated sequences of genome using next generation sequencing (NGS). And then we analyzed the integration sites by two methods with the NGS results, HPV Detector. We applied the study on 17 patient samples, 15 of them were found HPV16 positive and 2 of them were found HPV18 positive. Among them 16 were detected with HPV integration sites. Results: The results indicated that different samples showed different numbers of integration sites with limited overlapped positions in genome. The integrated positions of HPV16/18 located in all the genes of the virus, but mostly distributed in gene E1, L1 and L2. We identified integration sites HPV16 E6/GATC，E6/WWTR1，L2/DGKB, E1/EHHADH, ect. Some of the integrated sites in human genome are belong to intergenic region. We also used cancer gene panel, which cover 143 cancer related genes exon regions, to identify the mutation sites of each samples. We summed up a highly occurred mutated cancer gene list, which include ALK, NF1, PIK3R1, ROS1, TSC1, TSC2, ect. Most of them are either cancer driver genes or have been found highly related to cervical cancer. Further study is still carrying on. Conclusions: In conclusion, our HPV probe could successfully detect HPV16 and HPV18 in patient samples and enrich HPV integration sites in human genome of cervical samples significantly. It could provide detailed information for cervical cancer discovery and early detection.