This article sets out to investigate the psychiatric and psychosocial risk factors for high risk sexual behaviour in a war-affected population in Eastern Uganda. A cross-sectional survey was carried out in four sub-counties in two districts in Eastern Uganda where 1560 randomly selected respondents (15 years and above) were interviewed. The primary outcome was a derived variable "high risk sexual behaviour" defined as reporting at least one of eight sexual practices that have been associated with HIV transmission in Uganda and which were hypothesised could arise as a consequence of psychiatric disorder or psychosocial problems. Multivariable logistic regression was used to assess factors associated with high risk sexual behaviour in this population. Males were more likely to have at least one "high risk sexual behaviour" than females (11.8% vs. 9.1% in the last year). Sex outside marriage was the most commonly reported high risk sexual behaviour. Among males, the factors independently associated with high risk sexual behaviour were: being married, belonging to non-Catholic/non-Protestant religions, poverty, being a victim of intimate partner violence and having a major depressive disorder (MDD). Among females, the factors that were independently associated with high risk sexual behaviour were: being in the reproductive age groups of 25-34 and 35-44 years, not seeing a close relative killed and having experienced war-related sexual torture. Holistic HIV/AIDS prevention programming in conflict and post-conflict settings should address the psychiatric and psychosocial well-being of these communities as a risk factor for HIV acquisition.