BACKGROUND: Conflict and post-conflict communities in sub-Saharan Africa have a high under recognised problem of intimate partner violence (IPV). Part of the reason for this has been the limited data on IPV from conflict affected sub-Saharan Africa. This paper reports on the prevalence, risk factors and mental health consequences of IPV victimisation in both gender as seen in post-conflict eastern Uganda. METHODS: A cross-sectional survey was carried out in two districts of eastern Uganda. The primary outcome of IPV victimisation was assessed using a modified Intimate Partner Violence assessment questionnaire of the American Congress of Obstetricians and Gynaecologists. RESULTS: The prevalence of any form of IPV victimisation (physical and/or sexual and/or psychological IPV) in this study was 43.7 % [95 % CI, 40.1-47.4 %], with no statistically significant difference between the two gender. The factors significantly associated with IPV victimisation were: sub-county (representing ecological factors), poverty, use of alcohol, and physical and sexual war torture experiences. The mental health problems associated with IPV victimisation were probable problem alcohol drinking, attempted suicide and probable major depressive disorder. CONCLUSION: In post-conflict eastern Uganda, in both gender, war torture was a risk factor for IPV victimisation and IPV victimisation was associated with mental health problems.