Summary Background Concerns have been raised about the psychological effect of continued combat exposure and of repeated deployments. We examined the consequences of deployment to Iraq and Afghanistan on the mental health of UK armed forces from 2003 to 2009, the effect of multiple deployments, and time since return from deployment. Methods We reassessed the prevalence of probable mental disorders in participants of our previous study (2003–05). We also studied two new randomly chosen samples: those with recent deployment to Afghanistan, and those who had joined the UK armed forces since April, 2003, to ensure that the final sample continued to be representative of the UK armed forces. Between November, 2007, and September, 2009, participants completed a questionnaire about their deployment experiences and health outcomes. Findings 9990 (56%) participants completed the study questionnaire (8278 regulars, 1712 reservists). The prevalence of probable post-traumatic stress disorder was 4·0% (95% CI 3·5–4·5; n=376), 19·7% (18·7–20·6; n=1908) for symptoms of common mental disorders, and 13·0% (12·2–13·8; n=1323) for alcohol misuse. Deployment to Iraq or Afghanistan was significantly associated with alcohol misuse for regulars (odds ratio 1·22, 95% CI 1·02–1·46) and with probable post-traumatic stress disorder for reservists (2·83, 1·23–6·51). Regular personnel in combat roles were more likely than were those in support roles to report probable post-traumatic stress disorder (1·87, 1·26–2·78). There was no association with number of deployments for any outcome. There was some evidence for a small increase in the reporting of probable post-traumatic stress disorder with time since return from deployment in regulars (1·13, 1·03–1·24). Interpretation Symptoms of common mental disorders and alcohol misuse remain the most frequently reported mental disorders in UK armed forces personnel, whereas the prevalence of probable post-traumatic stress disorder was low. These findings show the importance of continued health surveillance of UK military personnel. Funding UK Ministry of Defence.