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The extent to which highly active antiretroviral therapy (HAART) affects human papillomavirus (HPV) acquisition and clearance in HIV-infected women is not well understood. We sought to describe high-risk HPV detection and clearance rates over time since HAART initiation, based on time-varying HIV viral load (VL) and CD4 T-cell count, using novel statistical methods.We conducted a retrospective analysis of data from the completed AIDS Clinical Trials Group (ACTG) A5029 study using multi-state Markov models. Two sets of high-risk HPV types from 2003 and 2009 publications were considered.There was some evidence that VL > 400 HIV-1 RNA copies/mL was marginally associated with a higher rate of HPV detection [P = 0.068; hazard ratio (HR) = 4.67], using the older set of high-risk HPV types. Such an association was not identified using the latest set of HPV types (P = 0.343; HR = 2.64). CD4 count >350 cells/μL was significantly associated with more rapid HPV clearance with both sets of HPV types (P = 0.001, HR = 3.93; P = 0.018, HR = 2.65). There was no evidence that HPV affects VL or CD4 cell count in any of the analyses.High-risk HPV types vary among studies and can affect the results of analyses. Use of HAART to improve CD4 cell count may have an impact on the control of HPV infection. The decrease in VL may also have an effect, although to a lesser degree.