The genetic variability of E6, E7 and L1 of HPV81 from HIV-1 positive women carrying multiple HPV infections was investigated by clonal analysis for E6 and E7. The range of maximal divergence from the prototype was 0.6%-2.6% for E6 and 1.0%-3.1% for E7. Compared to prototype HPV81, 13 and 10 mutations were identified in E6 and E7, respectively. In the pRB binding domain of E7, all HPV81 clones showed D21, as reported for prototype HPV81 and for HPV16 and 18, while G22 is reported in HPV6 and 11. In the CR3 region, CxxC motif was conserved in all but one clone. The L1 sequence of a single clone from 5 study patients was also established. The range of similarity with prototype HPV81 was 97.8%-99.2%, with 25 polymorphic sites. Two substitutions (R492K and T493S) were observed in 5/5, one (T287N) in 4/5 patients. Among L1 immune-related regions, BC loop presented T56N in 1/5, while FGb loop presented T287N in 4/5 patients. Our data indicate the presence of polymorphisms in all 3 HPV81 genes analyzed, with a certain degree of intra-patient diversity. The importance of polymorphisms on HPV81 persistence and pathogenicity needs to be addressed in longitudinal studies involving larger patient numbers.