Despite growing knowledge of the dynamics of HIV infection during conflict, far less is known about the period that follows cessation of hostilities and its implications for population health. This study sought to fill a lacuna in epidemiological evidence by examining HIV infection and related vulnerabilities of young people living in resource-scarce, post-emergency transit camps that are now home to thousands of displaced people following two decades of war in northern Uganda. In 2010, a cross-sectional demographic and behavioural survey was conducted with 384 transit camp residents aged 15-29 years old in Gulu District. Biological specimens were collected for rapid and confirmatory HIV testing. Separate multivariable logistic regression models by sex identified risk factors for HIV infection. HIV prevalence was 15.6% (95% confidence interval [CI]: 10.8%, 21.6%) among females and 9.9% (95% CI: 6.1%, 15.0%) among males. The strongest correlate of HIV infection among men was a non-consensual sexual debut (adjusted odds ratio [AOR] 3.24; 95% CI: 1.37-7.67), and having practiced dry sex (AOR 7.62; 95% CI: 1.56-16.95) was the strongest correlate among women. Conflict-affected men and women experience vulnerability to HIV infection in different ways than may have originally been understood. Post-conflict programme planners must therefore design and implement contextualised, evidence-based responses to HIV that are sensitive to gender and cultural issues.