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Background: Conflict and humanitarian crises increase the risk of both intimate partner violence and non-partner sexual violence against women and girls. We measured the prevalence and risk factors of different forms of violence against women and girls in South Sudan, which has suffered decades of conflict, most recently in 2013. Methods: A population-based survey was conducted among women aged 15–64 in three conflict-affected sites in South Sudan: Juba, Rumbek, and the Protection of Civilian Sites (PoCs) in Juba between 2015 and 2016. Findings: A total of 2,244 women between the ages of 15–64 were interviewed. Fifty percent (in the Juba PoCs) to 65% (in Juba and Rumbek) of all female respondents experienced either physical or sexual violence from a partner or non-partner in the course of their lifetimes. Approximately 35% of respondents have experienced rape, attempted rape or other forms of sexual violence by a non-partner during their lifetime. For ever-partnered women, lifetime prevalence of physical and/or sexual partner violence ranged between 54% in the Juba PoCs and 73% in Rumbek. Restrictive marital practices and gender norms, and experiences of conflict were major drivers of both partner and non-partner violence. Conclusion: Women and girls in South Sudan suffer among the highest levels of physical and sexual violence in the world. Although the prevalence of sexual assault by non-partners is four times the global average, women are still at greatest risk of physical and sexual assault from intimate partners. Conflict-related and intimate partner violence reinforce each other and are upheld by restrictive gender norms and marital practices. Expansion of comprehensive services, including health and psycho-social support for survivors is urgently needed. Moreover, policies and laws to prevent violence against women and provide survivors with access to justice should be given high priority within the ongoing peacebuilding process in South Sudan. [ABSTRACT FROM AUTHOR]