The prevalence of human papillomavirus genotypes differs in various target organs. HPV16 is the mostprevalent genotype in the cervix while genotypes 6 and 11 are highly prevalent in skin and aero-digestive tractinfections. In this study HPV11 positive specimens were selected from cervix, larynx and lung biopsy tissueto analyze the whole genome by PCR and direct sequencing. Five HPV11 whole genomes were characterized,consisting of two cervical specimens, two laryngeal specimens and one lung specimen. The results showed highhomology of HPV11 in these organs. Phylogenetic analysis showed that all HPV11 derived from various organsbelonged to the same lineage. Molecular characterization and functional studies can further our understandingof virulence, expression or transmission. Additional studies on functional protein expression at different organsites will also contribute to our knowledge of HPV infection in various organs.