Hu et al. analysed 130 samples of cervical intraepithelial neoplasia and cervical carcinoma, and identified human papillomavirus (HPV) integration sites. They confirmed previously reported integration sites and also identified new ones. In addition, they uncovered changes in gene expression resulting from viral integration, including increased levels of MYC. Importantly, they found that there were sequence microhomologies between the HPV genome and the integration sites, strongly indicating that viral integration occurs via microhomology-mediated DNA repair.