BACKGROUND: Concerns have been raised about the mental and physical health of UK military personnel who deployed to the 2003 war in Iraq and subsequent tours of duty in the country. METHODS: We compared health outcomes in a random sample of UK armed forces personnel who were deployed to the 2003 Iraq war with those in personnel who were not deployed. Participants completed a questionnaire covering the nature of the deployment and health outcomes, which included symptoms of post-traumatic stress disorder, common mental disorders, general wellbeing, alcohol consumption, physical symptoms, and fatigue. FINDINGS: The participation rate was 62.3% (n=4722) in the deployed sample, and 56.3% (n=5550) in the non-deployed sample. Differences in health outcomes between groups were slight. There was a modest increase in the number of individuals with multiple physical symptoms (odds ratio 1.33; 95% CI 1.15-1.54). No other differences between groups were noted. The effect of deployment was different for reservists compared with regulars. In regulars, only presence of multiple physical symptoms was weakly associated with deployment (1.32; 1.14-1.53), whereas for reservists deployment was associated with common mental disorders (2.47, 1.35-4.52) and fatigue (1.78; 1.09-2.91). There was no evidence that later deployments, which were associated with escalating insurgency and UK casualties, were associated with poorer mental health outcomes. INTERPRETATION: For regular personnel in the UK armed forces, deployment to the Iraq war has not, so far, been associated with significantly worse health outcomes, apart from a modest effect on multiple physical symptoms. There is evidence of a clinically and statistically significant effect on health in reservists.