Background Residents of the Republic of Serbia faced civil war and a NATO-led bombing campaign in 1999. We sought to assess the burden of metal health dysfunction among emergency department (ED) patients presenting for care three years post-war in Serbia. Methods This study was conducted during July and August 2002 at two sites: a university hospital ED in Belgrade, Serbia and an ED in a remote district hospital serving a Serbian enclave in Laplje Selo, Kosovo. Investigators collected data on a systematic sample of non-acute patients presenting to the ED. All respondents completed a structured questionnaire assessing demographics and symptoms of post-traumatic stress disorder (PTSD) (using the Harvard Trauma Questionnaire), and major depression (using the Center for Epidemiologic Studies Depression Scale). Results A total of 562 respondents participated (310 in Belgrade, 252 in Laplje Selo); the response rate was 83.8%, 43% were female, and mean age was 37.6 years (SD = 13.4). Overall, 73 (13.0%) participants had symptoms consistent with PTSD, and 272 (49.2%) had symptoms consistent with depression. Sixty-six respondents had both disorders (11.9%). In separate multivariable logistic regression models, predictors of PTSD were refugee status and residence in Laplje Selo, and predictors of depression were older age, current unemployment, and lower social support. Conclusions Three years post-war, symptoms of PTSD and major depression in Serbia remained a significant public health concern, particularly among refugees, those suffering subsequent economic instability, and persons living in rural, remote areas.