Respiratory tract tissues containing latent human papillomavirus (HPV) 11 were analyzed by reverse transcription-polymerase chain reaction for the presence of viral-specific RNA from the early region of the genome and compared to a similar analysis of laryngeal papillomas. Latently infected tissue contained low-abundance transcripts that could code for E1 and E2 proteins, but lacked evidence of spliced transcripts for the E6 and E7 proteins. Both latently infected tissue and papilloma tissue contained low-abundance antisense transcripts. Cultured cells infected with HPV 11 virions or transfected with HPV DNA, and cells derived from latently infected tissue, expressed transcripts similar to those seen in papillomas, but at a lower abundance. We postulate that latency is determined by the absence of or limiting levels of critical viral proteins.