Emerging evidence supports the role of human papillomavirus (HPV) intratype variations in the development of cervical lesions in immunocompetent women, but few studies investigated HPV16 variants in human immunodeficiency virus (HIV)-positive women. This is the first study in Brazil evaluating HPV16 variants in women with (n = 19) and without (n = 22) HIV infection, as well as cervical lesions. Although non-European variants presented an almost 3-fold increase (13.6% vs. 36.8%) among HIV-positive women, associations between HPV16 variants and HIV infection did not reach statistical significance (Fisher's exact test, p = 0.15). No associations were found between non-European variants and HSIL (Fisher's exact test, p = 0.41), although a significant association was observed between European variants and HSIL among HIV-negative women (Fisher's exact test, p = 0.01). In conclusion, in HIV-negative women the HPV16 European variants seem to influence the occurrence of HSIL, whereas in HIV-positive women, similar roles are atributted to both variants.