Among 544 HIV-positive women screened for HPV-DNA between 2003 and 2005, 265 (48.7%) were HPV-positive: 24 (9.1%) harboured HPV-16, 21 (7.9%) HPV-31, 12 (4.5%) HPV-18, 7 (2.6%) HPV-33. E6 and E7 of these HPV types were sequenced to assess their diversity. Ranges of inter- and intra-variant diversity were 1.2-3-3%, and 0.8-1.8 for E6 and 0.6-2.7%, and 0.6-2.0% for E7, respectively. HPV-31, the second most common HPV type, showed the highest diversity for both regions. On the whole, 26 out of 59 mutations were non-synonymous. The variability of these proteins may have implications in HPV vaccine strategies.