BACKGROUND: Despite significant research examining mental health in conflict-affected populations we do not yet have a comprehensive epidemiological model of how mental disorders are distributed, or which factors influence the epidemiology in these populations. We aim to derive prevalence estimates specific for region, age and sex of major depression, and PTSD in the general populations of areas exposed to conflict, whilst controlling for an extensive range of covariates. METHODS: A systematic review was conducted to identify epidemiological estimates of depression and PTSD in conflict-affected populations and potential predictors. We analyse data using Bayesian meta-regression techniques. RESULTS: We identified 83 studies and a list of 34 potential predictors. The age-standardised pooled prevalence of PTSD was 12.9% (95% UI 6.9-22.9), and major depression 7.6% (95% UI 5.1-10.9) - markedly lower than estimated in previous research but over two-times higher than the mean prevalence estimated by the Global Burden of Disease Study [3.7% (95% UI 3.0-4.5) and 3.5% (95% UI 2.9-4.2) for anxiety disorders and MDD, respectively]. The age-patterns reveal sharp prevalence inclines in the childhood years. A number of ecological variables demonstrated associations with prevalence of both disorders. Symptom scales were shown to significantly overestimate prevalence of both disorders. Finding suggests higher prevalence of both disorders in females. CONCLUSION: This study provides, for the first time, age-specific estimates of PTSD and depression prevalence adjusted for an extensive range of covariates and is a significant advancement on our current understanding of the epidemiology in conflict-affected populations.