BackgroundThis study aims at evaluating the cost-effectiveness of a 2-dose schedule human papillomavirus (HPV) vaccination programme of HPV and human immunodeficiency virus (HIV) naïve 12-year-old girls, in addition to cervical cancer (CC) screening alone, in South Africa. The study aims to account for both the impact of the vaccine among girls who are HIV-positive (HIV+) as well as HIV-negative (HIV-) population.MethodsA previously published Markov cohort model was adapted to assess the impact and cost-effectiveness of a HPV vaccination programme in girls aged 12 years (N = 527 900) using the AS04-adjuvanted HPV-16/18 vaccine from a public payer perspective. Two subpopulations were considered: HIV- and HIV+ women. Each population followed the HPV natural history with different transition probabilities. Model input data were obtained from the literature, local databases and Delphi panel. Costs and outcomes were discounted at 5 %. Extensive sensitivity analyses were conducted to assess the robustness of the evaluation.ResultsImplementation of the AS04-adjuvanted HPV-16/18 vaccine in combination with current cytological screening in South African girls could prevent up to 8 869 CC cases and 5 436 CC deaths over the lifetime of a single cohort. Without discounting, this HPV vaccine is dominant over screening alone; with discounting, the incremental cost-effectiveness ratio is ZAR 81 978 (South African Rand) per quality-adjusted life years (QALY) gained. HPV vaccination can be considered cost-effective based on World Health Organization (WHO) recommended threshold (3 x gross domestic product/capita = ZAR 200 293). In a scenario with a hypothetical targeted vaccination in a HIV+ subpopulation alone, the modelled outcomes suggest that HPV vaccination is still cost-effective, although the incremental cost-effectiveness ratio increases to ZAR 102 479. Results were sensitive to discount rate, vaccine efficacy, HIV incidence and mortality rates, and HPV-related disease transition probabilities.ConclusionsThe AS04-adjuvanted HPV-16/18 vaccine can be considered cost-effective in a South African context although the cost-effectiveness is expected to be lower in the HIV+ subpopulation than in the overall female population. With improved access to HIV treatment, the HIV mortality and incidence rates are likely to be reduced, which could improve cost-effectiveness of the vaccination programme in South Africa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-1295-z) contains supplementary material, which is available to authorized users.