Consensus primer mediated PCR protocols have the potential to amplify previously uncharacterized human papillomavirus (HPV) genotypes. In a study on 500 cervicovaginal samples, we amplified four sequences (L1AE 1 to L1AE 4) that failed to hybridize to any of the available HPV type-specific oligonucleotide probes. Nucleotide sequencing revealed that the sequences were derived from the L1 region of hitherto unsequenced genotypes. Comparison of phylogenetic trees based on the amplified L1 sequences with E6-derived phylogenetic trees resulted in the identification of L1AE 1 and L1AE 2 as putative novel HPV PCR genotypes. L1AE 1 was related to HPV 39, whereas L1AE 2 was related to HPV 51. The L1AE 3 and L1AE 4 sequences occupied L1-phylogenetic branches equivalent to the positions of HPV 66 and HPV 61, respectively, in an E6-phylogenetic tree.