Can contemporary female HIV rates be traced back to women’s position in ancestral societies ? In matrilineal kinship organizations, lineage and inheritance are traced through female members and children integrate the kin group of their mother rather than their father. Ethnographic accounts suggest that in matrilineal kinship structures, women benefit from greater autonomy and spousal cooperation is reduced. I test the hypothesis that, by affecting women’s sexual and contraceptive behaviours, ancestral matrilineality has a causal impact on the prevalence of female HIV. Using variation in ethnic groups’ ancestral kinship organizations within Sub-Saharan African countries, I find that females originating from ancestrally matrilineal ethnic groups are today more likely to be infected by HIV. This finding is robust to the inclusion of subnational fixed effects, as well as a large set of cultural, historical, geographical, and environmental factors. I find consistent results using a number of alternative estimation strategies, including a geographic regression discontinuity design at ethnic boundaries and an instrumental variable strategy. Matrilineal females’ riskier sexual and contraceptive behaviours constitute the main explanatory mechanisms. These results call for policies moving beyond the “one-size-fits-all” strategy and taking local cultural contexts into account.