This Discussion Paper examines the linkages between gender and gender inequality in the context of conflict, sexual violence and HIV transmission, and their impact on post-conflict reconstruction in Sierra Leone and Liberia. It makes two critical contributions to a gendered perspective on post-conflict transitions in West Africa. First, it notes that contrary to conventional wisdom, post-war transitions to relative peace have made little difference to women's exposure to chronic sexual violence, with potential implications for increased HIV transmission. Second, the study interrogates those assumptions linking war-related sexual violence to high HIV prevalence in post-conflict contexts, by showing that despite over a decade of armed conflict, Liberia and Sierra Leone had adult HIV prevalence rates among the lowest in West Africa. This paper goes beyond generally held notions of the sexual and gender dimensions of civil wars in Africa and points to a gap in and key challenge for studies and policies on post-conflict reconstruction in Africa.