Cervical specimens obtained from previous clinical studies at the University of New Mexico were screened for reference strain human papillomaviruses (HPVs) via HPV L1 consensus polymerase chain reaction (PCR) and type-specific oligonucleotide probe hybridization. PCR products that bound to an HPV generic probe but did not hybridize with HPV type-specific oligonucleotide probes were subjected to restriction endonuclease digestion analyses. Resulting restriction fragment length polymorphisms served as the basis for initial grouping of unknown HPVs and identification of potential reference strain HPV variants. MY09/MY11 PCR products containing putative novel HPV L1 fragments were cloned and sequenced. Five novel HPV sequences were identified in this study.