Papillomaviruses are responsible for a variety of diseases in humans and animals, ranging from harmless skin warts to lethal cancers. They also make up one of the most genetically diversified families of viruses known, and could represent a model system of DNA-virus evolution. A specialized genetic sequences database, The Human Papillomavirus Database and Analysis Project, was recently established in an effort to provide database services that are specific to papillomaviruses to the research community and to perform a variety of sequence-based analyses. This review is intended to present the scope of the information currently contained in the database and to outline some of the analyses that have been performed on the genetic sequences. These analyses will address issues including phylogenetic relationships, recombination events, selective pressures on different genes and the possibility of cross-species transmission in the case of the papillomaviruses.