Human papillomaviruses (HPVs) are etiologic agents of benign and malignant tumors of the skin and mucosal surfaces. The life cycles of HPVs are dependent upon the differentiation of the epithelial cells they infect. The organotypic (raft) tissue culture system supports epithelial differentiation in vitro and permits the analysis of HPV life cycles. The structures and temporal expression patterns of HPV transcripts, temporal expression from viral promoters, and changes in genome replication during the viral life cycle can be studied in raft tissues derived from cells that maintain episomal copies of HPV genomes. Most of the transcriptional data on the HPV life cycle have come from analyses of the CIN-612 9E cell line grown in the raft system. CIN- 612 9E cells stably maintain episomal genomes of HPV31b, a virus type associated with cervical cancers. HPV31b has been shown to express twelve early gene and twenty late gene RNAs from eight viral promoters. The virus employs five promoters which are constitutively active, albeit at different levels, throughout the viral life cycle. Two promoters in the upstream regulatory region (URR), a non-coding region of the viral genome, are negatively affected by epithelial differentiation. A differentiation-induced promoter appears to be responsible for the large induction of late gene transcripts encoding the capsid proteins in the highly differentiated cells of the epithelium. E1 and E2 gene products are important for viral DNA replication, and an increased ratio of E1 to E2 transcripts correlates with the peak in vegetative viral DNA replication observed in the raft tissue culture system. The maximal expression of late gene transcripts and amplification of viral DNA are coincident with the appearance of virus particles in the raft tissues.