Most countries rely on anonymous antenatal surveys to generate HIV seroprevalence data for women of reproductive age. These data is often used as surrogate markers for HIV prevalence rates in men of a similar age. The seroprevalence of HIV among pregnant women differs remarkably around the continent, with the highest rates being seen in Southern Africa, as high as 30%, and much lower rates being seen in West Africa. These reasons underlying these differences are complex and not completely understood.

UNAIDS estimated in 2005 that 470 000 (87%) of the world's 540 000 newly infected children (<15 years old) reside in Sub-Saharan Africa. Prevention of mother to child transmission (PMTCT) of HIV is thus a national priority in many Sub-Saharan African countries. Despite policies, treatment is sometimes not given at the clinic level for several reasons, and when it is, most commonly it is with single dose Nevirapine. Data from South Africa has shown that both mothers and infected babies rapidly acquire nevirapine resistance. It is likely that this will lead to early failure of first line antiretroviral (ARV) therapy among these mothers once they start their ARVs. In South Africa, for example, either efavirenz or nevirapine form the backbone of the first-line ARV regimens.

AIDS defining illnesses (ADIs) in women living in Africa are similar to those observed in men. Tuberculosis is the most common ADI but other life-threatening illnesses such as cryptococcal meningitis are relatively common compared to other parts of the world. Cervical cancer and cervical intra-epithelial neoplasia (CIN) lesions are more common in HIV-infected than in non-infected women. Most countries in Africa do not have cervical screening programmes and, even in richer countries such as South Africa, the national policy is to screen women three times in their life at 30, 40 and 50 years of age. Many HIV specialist centres, with additional donor funds, are now attempting to perform annual cervical screening, at least in South Africa.